Re: no spark
If I understand correctly, you pulled an engine out of a car that was an automatic and installed it in your car that is a stick? Should be pretty straight forward. Did you use the harness from the old engine? I would guess it is either a difference in the wiring, or a missed connection somewhere. Check the grounds, connections, fuses and safety switches. As far as the engine itself, there really shouldnt be any differences other than those you have already addressed.