Input - the thing that the torque converter acts upon to create a phase change in the transmission's internal parts resulting in the transfer of kinetic energy from the engine to the planetary gear set, and eventually driving the wheels.
You'll find it once you pull the transmission and remove the torque converter.
Alternatively, you can look at a this:
3100 or 3400 with a stick shift? - Page 2 - Grand Am Owners Club Forums, or this:
How do you determine 4T60E final ratio (2.73, 2.97, 3.33)? - Cadillac Owners Group to get some ideas.
Seems that you can use a 5 speed from the Quad-4 4 cylinder if you change the front half of the transmission case, don't know if that's an option for you, but it has a nice FDR.
If it's not an option, you might look into learning to rebuild an Auto tranny for the longer gears.
The PCM thing is just a matter of taking the chip from the PCM of the car you took the transmission from, or having someone flash yours. The longer FD will make the PCM think that it's not shifting properly.
I'm sure if you wanted to build a tranny from the case up, you could make an interesting combo of gears and FD to make a great tranny for both city and highway driving.