Here is a discussion over on
the gpspassion forum about changing the nav software on another WinCE based gps device. You can get an idea about how difficult it might be. I didn't read the whole thing, but it sounds like you need to modify the unit's firmware so that you can get access to the WinCE file system, in order to load new software. Good luck with that.
When your unit does a cold start, do you see any type of BIOS messages, or any indications that WinCE is loading? Is it possible to disrupt the normal boot sequence and get into the OS?
Basically, what you need to do is load the new nav software in place of the one that's currently loaded, and then find out how to access the NMEA stream from the internal gps module.