Mike,
Seeing as how the only change that i know that you made so far is the injectors and the comp, back track, disconnect the comp box first , try that. If the idle is at 600 , chances are you have an injector tube issue, it is possible you nicked more than the one you thought you did.
Best way to check is make sure the idle is nice and smooth. With a set of DD 11's your idle should be very smooth. In other words your tach should not be moving around.
Since I have your new transmission still on my bench, and the transmission hasnt been altered yet, chances are the trans is not the source of the problem.
I know turbo terry up there is struggling with a fuel issue, is it possible you got some bad fuel?
You may want to try and email terry , he is also a tdr member.