Rep Power: 0

I have a 96 honda civic si. Automatic transmission. 97cid (1.6 L)? Can i use any 1.6 L from any civic from 96-2000? And will a manual transmission engine work in my automatic car?

 
Rep Power: 168

You could swap the engines yes, it will be a pain because the SI has the B29, not the DY series, so there will be some minor differences.

And I can't say for sure, but from what I've heard, converting a car from automatic to manual is a very tough job and I've heard many people try to attempt this only to say their cars have never ran the same afterwards.