although i have an s13, with an s14 trans, i can answer a few of your questions.
the rev limiter works from engine revs, not the trans, then cuts the fuel to limit the revs. so yes it will still work. and to your question about it running well... yes, it runs great

no drawbacks except having to shift gears
for s14's you need to swap over the manual ecu in order for it to not throw diagnostic codes. s13s like mine, don't.. i still have my automatic ecu in.