You're going to some great lengths with an auto... It almost calls for a new car, but if you have the time and that patients (and especially the $$) I commend you.

This is one of the most asked questions on this board so you could do a search for compatible engines and find a bunch of info.

you can swap any B-series engine (B16A2, B16A3, B16B, B18A, B18C1, B18C5, B18C) using stock mounts and it will slip right in.

You can also put H-series engines in with a HASport mount kit.

As for OBD1, I just used an OBD2 engine and harness with an OBD1 ECU and all is well.

I'm not too experienced with auto/manual conversions, but there was just a thread open on it in the '92+ civic forum. Do a search on that too.

Hope it helps.