stock truck will work fine with a trans that has been built. however if you wanna make use of that built trans, you may wanna invest in a tuner/programmer to turn it up. many of the people on here are using efilive. there's a whole section dedicated to it. you can build your own tunes or even purchase built tunes from others....
looks like you already have an edge box. running a buil tranny will let you turn it all the way up without hurtin the trans. you can even go bigger at that point depending on how big you have the trans built to.....
as for reflash, i think some people/all people?? reset the taps on the trans so the new tranny will learn your tune and driving habits quicker.