Wanted to give an update on my findings
1) After visiting my local GM dealer and some emails later; you can bypass the Retain Accessory Power RAP and the Express Down Module EDM by disconnecting them and doing the following on the connector:
For the RAP jump A to B to D. (Pink to dark blue to brown)
For the EDM jump D to E. (Brown to Gray).
Caveat: This information came from two reliable sources. Ie. My local GM service/shop manager and Rob at shbox. They also said that you will lose some operative ability like the low coolant indicator control latching (check your coolant light) and there may be more. Try this at your own risk. I have not done this yet.
2) I also found an aftermarket fix for the windows and a nice write up at ls1.com. Autotrix window fix in pics
apparently the issues is so common that the aftermarket has an over the counter fix.
3) I have not done any of these options as of today. Early this AM, I replace the RAP module and my windows are currently working. I suspect in time, I will be going to the aftermarket fix.