Among various strategies: alternating feating/fasting or taking melatonin for jet-lag to reset one's internal clock, staying up all the night before to finish work [my current favorite] allowing one to sleep on the flight, drinking heavily [my previous favorite], and doing all the movies on the plane.) If you like to sleep, make sure you don't get put on the isle in front of passengers who will jostle you on their way past; if you like to walk around, make sure you don't stuck on the window behind sleeping people.
Even after you touch down at Narita, you're still looking at another five or so hours of ground travel, and that's assuming you don't get lost, miss a train, get on a wrong train, sleep past your stop, etc. (I've done all of these.) There is also a taxi service, www.fukushimakanko.co.jp/airport1.htm (but the charge is per passenger [not per car-load], and it seems more dangerous [private car racing along highway seems less secure than tracked train], and less environmentally friendly, so i haven't used it).
Guests often come a day earlier and spend the first night in Tokyo, to a) smooth the jetlag, and b) have a day to explore "The Big Orange."
If you decide not to overnight in Tokyo on the way in, there are several options regarding travel from the Narita airport.
Travelers who take the Keisei Skyliner from Narita switching to the SKS must go out of the Keisei terminal at Ueno and walk two blocks to the adjacent JR station. Even though the stations are close, the SKS tracks are in the bowels of the JR station, down about three escalators, so allow at least 10-15 minutes at a brisk, non-dawdling walk.) The SKS fare is about ¥8000 (about $80), and the trip takes about an hour and a half.
If you choose to overnight in Tokyo before coming to Aizu, to break apart the long trip, beat the jet-lag, and do some sight-seeing, there're many museums in Ueno park (art, science, history, etc.) so it's doubly compelling, depending on your plans for your transition day. There are various (comfortable, family-run) inns in Ueno, some in the shadow of Ameyoko Sundries Market, including Koyamatsu ([+81](3)3833-6821, but they don't speak much English) or Kiniuya. They're convenient and traditional (futon on tatami). These aren't luxury ryokans, but reasonably priced (maybe around ¥5,000). A fancy inn like you might have read about would normally cost at least twice that, but for such inns there is often an elaborate meal included and/or an onsen, neither of which such modest inns have (there might be breakfast included, and of course there is a shower/bath [perhaps with shared toilet facilities], but they aren't onsens). These inns are quite close to the train station, just a few minutes' walk.
Alternatively, if you want to stay in a hotel in Roppongi (a district famous for its nightlife and foreigners), check the departure time of the "limousine bus" towards Akasaka for either the ANA Hotel or the Grand Hyatt Tokyo Hotel in Roppongi Hills (It's the same bus; fare is ¥3000 [half price for children].): http://www.limousinebus.co.jp/e/timetable/narita/akasaka_h.html
If there is no convenient bus, then take the train in, as described above, then switch to the subway. From Ueno station, take the Hibiya Line to Roppongi (¥160). From Tokyo Station, take the Marunouchi Line to Kasumigaseki, then switch to the Hibiya Line to Roppongi (¥160). The subway map is posted at http://www.tokyometro.jp/e/index.html.
The JR Tohoku SKS (sign colors: dark green on creamy white) leaves from SKS tracks 22 and 23 in Tokyo Station, and goes through Ueno Station. The schedule (valid until 15 March, 2013) is posted at http://jreast-shinkansen-reservation.eki-net.com/pc/english/common/timetable/e_tohoku_d_b/index.html . (Note: the SKS ticket is good from anywhere within the Yamanote-sen, the JR line ringing Tokyo, so if you're coming from central Tokyo you needn't buy any other ticket, even if you don't get on at Tokyo Station or Ueno.) Make sure the train you get on stops at Kõriyama. The connection schedule is posted at http://www.aizu.com/train/index-e.html. The last SKS with a connection to Aizu leaves Tokyo Station at 20:56 (as of 4/2013, but best confirm the schedule to avoid surprise); other trains leave after that, but they get into Kõriyama too late for the local train. If you arrive too late in Kõriyama to get the local train (about which more below), you can stay in a business hotel, several of which are close to the station. I usually try to get into cars #1 or #2, which are non-reserved, non-smoking.
There is a "Green Car" on the SKS that is the equivalent of first class. I think its primary convenience is that the carriages are close to the escalator, as opposed to the regular coaches on the end of the train. Maybe the seats are roomier, but not significantly. Maybe the main attraction is that the higher price keeps out the riff raff. (Egalitarian that i am, i believe that you meet more interesting people in steerage, at least on trains!) Reserved non-"Green Car" seats on the shinkansen are also slightly more expensive than unreserved, but i rarely bother getting reserved seats unless i'm traveling during a peak period and/or with companions/relatives. Maybe unreserved is fine, unless you are nervous, in which case the incremental price isn't exorbitant.
For both the SKS and the local train, you have to put the tickets through the wicket upon entering the station (in two stages for the SKS: once to get into the station, and once to get into the SKS area) and surrender upon getting out. (To buy a Ban-etsu ticket in Kõriyama, only the SKS ticket is surrendered; the other is presented at the window upon purchasing the Kõriyama->Aizu-Wakamatsu ticket, unless you had already gotten the local train ticket previously, perhaps as part of a combined Tokyo [or Ueno] to Aizu-Wakamatsu "basic fare.") The SKS ticket might also need to be shown to the conductor en route. Don't lose your tickets, throw them away, or forget them on the train. (I've done all of these.) If you do, just explain to the worker at the wicket. (Your story is more credible if you are drunk, tired, or foreign. [I've been all of these, too.])
After taking the SKS to Kõriyama, go downstairs (escalator or stairs) to switch to the Ban-etsu local train to Aizu-Wakamatsu (¥1,110 if bought separately). Go to the end of the station towards the toilets (away from the soba noodles stand). Those interested in such novelties might enjoy the elevator with two doors oriented at right angles, adjoining the overpass on track #2. The local leg takes about an hour, with pleasant scenery. (Inawashiro Town, about half-way between Koriyma and Aizu-Wakamastu, sits between Bandai-san, the local volcanic mountain, and Inawashiro Lake, Japan's fourth largest lake.)
If there is no convenient train from Kõriyama to Aizu, don't forget to check the buses, too, [Japanese] schedules to which are posted at http://www.aizubus.com/highway/koriyama1_1.html. They leave from Platform #4 in front of the Kõriyama station, and cost ¥1,000 each way (slightly less than the train), with tickets available from the kiosk near the platform. If you get off the bus at Kita-Yanagihara (two stops after the bus leaves the highway, one stop before the Aizu-Wakamatsu station), it's only a ten minute walk to the university.
There is also a bus directly between Shinjuku and Aizu, Japanese schedules to which are posted at http://www.aizubus.com/highway/shinjuku1_1.html (which costs about ¥5,000), a discount (only ¥2,200) bus between Tokyo Station and Washington Hotel in Aizu, the Sakura Kanko "Byakko" ("White Tiger") line, http://www.489.fm/010/audutokyo.html, and, twice a day, a bus from Narita to Kõriyama (from which one would take the bus or train to Aizu), http://www.fukushima-koutu.co.jp/x/modules/TinyD2/index.php?id=13 (schedule here: http://www.fukushima-koutu.co.jp/ride/highway_bus/f-k-nair/nair-k-f.html). There is also a "luxury discount" option Sakura bus, which costs about ¥3,500. (The Sakura bus leaves from a parking lot a couple of blocks south of the Tokyo station on the Yaesu side, towards Tokyo International Forum, and goes to the Route Inn Hotel in Aizu; check the map for details.) Both buses take about 50% longer than the connecting trains, i.e. about 4.5 hours. They stop twice for 15 minutes at highway rest stops but there is no transfer. (Tip for those who like to drink and ride: there's no alcohol sold at the rest stops, so buy such refreshments before you board the bus.)
Arriving in Aizu-Wakamatsu station (usually the terminus, or (if coming by bus) Washington Hotel near the station, unless on a train which continues on to Kita-Kata), guests can take a #19 bus (or #4 course?) to the University (12 min.) or Matsunaga (25 min.) until services ends around 21:00, after which a taxi is recommended. (Fare: about ¥1000 to the University, almost ¥2000 to Matsunaga Sun Mart.)
The total one-way fare is almost $100 equivalent. Train schedule is here (http://www.u-aizu.ac.jp/clerk/ao/pd/cl-linkage/location/lg02_en.htm). Exact fares are indicated in the page http://www.u-aizu.ac.jp/location/access/access.html
There is also a bus that i sometimes take when going straight from the airport to Aizu. It goes (subject to schedule times) from airport terminal curbside to Utsunomiya or Omiya, both of which are on the SKS line to Kõriyama. It won't save any time or money, but sometimes one is so tired after the international flight that it is a relief to fall into the bus seat and defer for a couple of hours the switch, instead of dragging one's bags down to the train. So, instead of switching at Tokyo or Ueno, you'd board the SKS in Utsunomiya or Omiya, the terminus of whichever bus is ridden. The "Friendly Limousine Bus" is near the exit from the customs after baggage claim. Its signage is white letters on an orange background. (A bus directly to/from Aizu to Narita airport is planned, but hasn't started service yet.)
For late arrivals, there is also an overnight bus from Narita to Kõriyama: http://www.chibakotsu.co.jp/kousoku/fukushima.htm. These take about four hours.
Arriving at Aizu-Wakamatsu station, there are several hotels nearby (where guests visiting the University often stay): The Fuji Grand and α-1 ("Alpha-One") are just to the right of the station exit, the Toyoko Inn just to the left, and the Washington Hotel is directly in front of the station, 2 blocks and five minutes walking. (There are also, further away from the station, onsen [luxury spas] like Toho Onsen in Higashiyama, as well as many family-style inns. A long list of hotels in Aizu-Wakamatsu is available here.) To get to the University from the station, my usual algorithm is to see if there's a bus leaving soon taking a taxi otherwise. (It takes about 30-40 minutes to walk.)
On your way back, assuming you ever want to leave Aizu, most of the above links are bidirectional. If you have an early flight (late morning), you can overnight in Koriyama, to get the first SKS towards Tokyo. (There are many business hotels near Koriyama station.) If your flight is even earlier, you could overnight in Tokyo or even Narita on your way out. This last option is very civilized (decadently luxurious) and reasonably priced. There are several hotels near the airport, but i have used this one and recommend it (including its health club): http://www.toto-motors.co.jp/marroad/narita/eindex.htm