swap from auto to manual tranny.

I swapped a 5 speed manual into my 93 toyota .It has a 3.O litre V6 it came stock with a automatic. It doesn't seem like it has the power it should.It still has the controls for the automatic and we either have to leave it in neutral or park.I am wondering if the electronic controls need to be swapped or something.

That's a little vague, can you be a little more specific as to the problem ?
2WD or 4WD ?
4 cyl or 6 cyl ?