1991 - 4AFE 3-Speed Swap for a 4-Speed

I have a really good running 91 4afe 1.6L corolla. I just got a replacement 4afe auto transmission they gave me a four speed in stead of a 3 speed thats good for me. I want more miles to the gallon. The question I have Is what do I need to make this work. Different shifter/ linkage? Will my cumputer work on this system everything I have read is pretty much telling me it will work. Does anyone have any info in this that could help me?