Don't mind the typical noob post, Only reason I'm even considering what's in the thread title in the first place is because I recently bought a 2000 EX (Meaning OBD2B, oh boy) in near-perfect condition, was maintained all its life, I'm even the second owner. However, it's auto-tragic , and my goal is to make it to a nice well-rounded vehicle, should call for at least a B-series 5 speed. I've been doing a little bit of searching around with DIY's and FAQ's on converting automatic 92-00 Civics to stick shift, and swapping B series engines into already 5-speed chassis. However, what if I were to do both at the same time?
Not only that, but there's also the fact that my car is OBD2B, which to my understanding brings a lot of small troubles in the way involving swapping engines. I get the gist of just about most of what would go on in doing this (buying the right mounts/linkage/pedal assembly/ecu etc.), but I'm having cold feet about the small troubles getting in my way, such as a small missing or misaligned part, or some small issue(s) involving wiring/vaccuum that would prevent my car from starting.

Anyone care to share their stories/problems involving swapping a 5-speed B-series into an Auto 99-00 if it's even been done before? Or should I just reconsider my options?