Auto to manual ecu problems

[Hockey27925]

yo i need some help with my ecu problems. i had a 96 civic coupe ex autoamtic, and i got it converted to a manual about a year ago and it runs fine. the shop did something with the stock ecu to bypass it somehow and i am running my car on the stock automatic ecu. I tried to put a manual ecu in but it dont fit into the new plugs. Now i am doing a gsr swap and i cant put the gsr ecu in the slots because it won't fit. please help me if you know anything about ecu's