1) Don't discount the 2-strokes because you need to mix your gas. Mixing gas is ridiculously easy. If you have other reasons for wanting a 4 stroke that's fine, but don't let the little issue you mentioned matter.
2) I've never used a shift kit, but I also hear they are nice. Personally, I've not really ever found the need and to me it would seem to add complication to the system.
3) I think the rag joint method of attaching the drive gear to the rear tire is the cheapest, but poorest method. It's putting undo stress on your spokes and leads to warped rims. I've build several of these bikes and the three I currently own have all been converted to some hub driven method. If you get the shift kit, you won't need the drive gear anyway, but otherwise definitely get the adapter. I've converted my single speed bike to 68 spoke rims and attached the gear that bolts to their larger flanged hubs. Another bike is the Grubee GT2 which comes with the heavy duty axle that has a hub mounted drive gear. The third bike is in the process of being converted to using a disk brake adapter for the drive gear. The rag joint will get you going, but you'll want something better soon enough.
Incidentally, putting on the rag joint drive gear is WAY harder than mixing 2 stroke gas.
4) Get a nice rear rack and some Ortlieb Backroller Panniers ($119 from Rei). They're water proof, quick release and VERY durable. I use them on my road bike and have on occasion put them on one of the motorized bikes to carry groceries (2 12 packs of pop and 2 1 gallon jugs of milk on one occasion).
5) Stock these motors won't go more than 30mph on level ground so unless you plan on modifications or a lot of downhills you are probably ok with the monkey lights. Get a cheap red flasher for the rear and a white flasher for the front. If you plan on riding at night I'd opt for the Niterider series of lights but they're pretty expensive.
Hope this helps!