First time rebuild problems-trouble upshifting

You have to have a spring between the throttle valve and the governor valve for things to work right. The TF-2 kit comes with a spring to replace the stock spring but if none in the kit fit you need to put the stock spring back in. Another issue I see that can cause very high upshift speeds is there's a sleeve on the throttle valve and you can install it backwards. It has an offset ridge to hole the throttle valve in it's proper position and if it's installed backwards it holds the valve a lot farther in.

By your description saying you had a couple mystery springs left over it sounds like the valve body needs gone through by someone that knows them to get it sorted out, or just buy a different valve body and start over. This time take pics so you get everything put back where it belongs.