You mean S13SR black top right, not S14SR? In case of S13SR, yeah, all fine except type-x which have different pinouts on the same blue plug. S14SR ECU has totally different plug(grey) so you need to run the S14SR loom but will run the engine fine as long as you match AFM and injectors to ECU and o2 sensor to a lesser extent. S15SR is same as S14SR but coils have built in ignitors.
Yeah, just run whatever ecu plugs into whatever loom you have.
auto to manual is fine. The only thing I noticed is auto ecu will push the car along at idle happily whereas the manual one struggles along at 500rpm pushing the car up the slightly inclined driveway. Both times in 2nd gear with no throttle input.