I would use the 1D3,there are arguments the 1D4 need timing fixes,but its hit and miss.Either will likely work. in any case recap it, the capacitors are way past due.
i would use the 040 board for sure, but if just gaming, ram board is good enough for most games though.
3.1 roms are readily available at amiga kit etc, and are not too much.
tv with scart lead should do well.
shielding doesnt matter.
I prefer amiga kbds on my amigas so i cant recommend any adapters really.
Pc drives can be converted to work as amiga 880K drives pretty easily. there are many threads on the forums about it. PC drives will not work straight away w/o mods.
Most amiga floppys just need a good head cleaning and the stepper shaft re-greased. the grease gets hard and it quits working sometimes.
Sounds like you have cool projects. be sure to remove any leaking batteries now from A500+ and or some ram/clock boards with NiCD/NiMH batteries.
good luck!