Well an auto ecu does you no good, cause it'll throw a CEL for missing auto transmission lockup solenoid, and refuse to run, I believe.

Fuel curve probably is different, but better.

99 civic is an OBD2B harness, very important.

No honda ecu will run boost by itself (well, short answer, heeheh) but the P28 OBD1 is a great platform to start from, and then have a fuel managment system.

-PHiZ