You don't think those wires had anything to do with it?

This sounds like it'* the classic surging/chuggle problem...... I hope you can track down the cause, because some of us have had these symptoms for a while and still have no solution. My next course of action is to check my TPS voltage and install a tranny cooler. Keep trying different things until you get this worked out.

By your description I had that exact same problem... took a scan tool found the tranny was acting up, especially when getting hot.

Torque Clutch Converter was locking up, or not unlocking, something, took it to a tranny shop, they heard about the prob, and fixed it.

Shuddering no more.