I have a 99 Civic EX with a D16Y7 (long story), but I am using my Stock EX ECM and it cuts off around 5400RPM and it slightly bogs off idle. Would a 99-2000 LX or DX ECM be a direct plug in and cure these problems? I tried a 96 D16Y7 ECM but the one of the connectors was different.

 

Yes a 99-00 DX-LX ecm would be compatible. The 96 has a different OBD than the 99.