Did the torque converter come out at all when you had them separated? If so, are you sure you got it back in properly? Check this thread and look at the pump tangs when it's not put in right.
There seems to of been an unfortunate trend lately with people having transmission related issues, causing them to have to drop theirs. I've installed and removed the 4L60E a handful of times now on several GMT360's. During my times spent doing so, I've learned a few key things to look out for...
gmtnation.com
The way to tell if it's the pump, pull the top tranny cooler hose, attach a hose to the end and put the other end into a container. Start the engine and see if you have a good steady stream.
Even with the connector disconnected, it will go into a gear as a default mode to get you home.