1. The FE2 uses two LR44 batteries. These are 1.5 Volt button cells, 11.4mm diameter and 5.2mm in height which are widely available - they are used in watches, calculators, etc.
2. Nikon still sells some manual focus lenses - see http://imaging.nikon.com/lineup/lens/list.htm#manual. However most photo shops won't stock them. You would either have to get them on special order, or mail order them from somewhere like bhphoto.com. Zeiss also makes a range of excellent manual focus lenses. The Zeiss "ZF" and "ZF2" lenses are designed for the Nikon F mount which the FE2 has (that's the "F" in "FE2"). Get the ZF2 lenses since they are optically identical to the ZF lenses but are also compatible with more modern Nikon cameras (see http://lenses.zeiss.com/photo/en_DE/...450.usage.html - you can click the icons under the pic to show info about the various lenses in the range). Also, current Nikon autofocus lenses will also work on the FE2 provided they have an aperture setting ring on the lens. Many of the recent lenses, with official names that end in "G" (e.g. Nikkor AF-S 50mm f/1.4G) don't have aperture rings. They rely on electronic aperture control by the camera body, which the FE2 does not support. However I would prefer manual focus lenses - they are cheaper (if purchased second hand), generally have a smoother manual focus action, and are usually smaller and lighter. Some of the more recent AF lenses also don't have good focus distance and depth of field markings, which are very helpful if you ever want to do landscape photography. If you want new and can afford it, get Zeiss ZF2 lenses. They're beautifully built and optically excellent. Otherwise second hand Nikon lenses from a trustworthy source like keh.com will do just fine.
3. The FE-2 will give TTL flash control with Nikon's last generation of flashes, the SB-600 and SB-800. AFAIK this won't work with the current SB-700 and SB-900 since they no longer support TTL, only i-TTL which is the digital camera equivalent. You should still be able to use these on manual, though I haven't tried it. The SB-600 is widely available on the used market and is a good, moderately priced flash - I have one.