OK After I did the 4.0 to 4.2 swap and found a couple of vacuum leaks, I took the car out for a short test drive. The motor idles like it has a big cam and puts out tons of power when you step on it. The problem I have is it only drives in what I think is 2nd gear. Goes in park, reverse and drive and will down shift if you stomp on it, but will not shift up to higher gears. I probably have not connected something right but can't figure out what it would be. I did not pull the trans when I did the swap. Any info to look in the right direction would be great. thanks steve

 

I assume that the trans was working properly before the swap? Shifting through all the gears, etc.

Maybe you could try a hard reset now that your vacuum leak and all that is fixed. Is the battery good and strong? These cars are prone to electrical misbehavior.

Do the sport button and J shifter side of the lever work? Thinking here is that maybe you have a slight adjustment problem on the shifter cable.

I don't have a 5spd but as I recall putting it in sport causes the car to start in gear 1. Does it up shift 1-2 in that case and then not to 3?