Thanks for the suggestions regarding replacement of the registry for the module
paths. They didn't directly solve my problem, but did lead me to some ideas
that eventually did the trick.
The trick was that the module name and the dll's pointed to in the module
registry could be renamed into the directly referenced name and also renamed as
.pyd files. I could then control the path of those imports
For example:
module pywintypes was referenced to C:\WINDOWS\SYSTEM\PyWinTypes15.dll
This just gets renamed to pywintypes.pyd