You do have to repin the ecu connectors, and there are a few other modifications that you have to make. If you're running the Silvertop AT ecu, the ecu pinouts are almost identical. Of course you have to run the Map and Iat sensors instead of the afm. Fortunately a map sensor from just about any corolla will work. 5sfe Celica map sensors work well also. Just about any toyota IAT sensor works fine.
I'm running blacktop electronics on my silvertop, and like it better. A higher revlimiter, a bit better topend, and the option to run stacks.
When I do 20v wiring harnesses for mr2's and ae86's, running a silvertop on blacktop electronics is a popular option. The nice thing about running BT electronics with the ae86 is that you don't have to get a custom airbox made.
I also make an ST to BT adapter. It takes almost all of the wiring out of the switchover.