I tried again this morning eliminating as many potential problems as possible. Redownloaded the original zip file to a different computer, unzipped the package, and then unzipped the first portion of the install onto a second freshly formatted flash drive. I went down to my car, used the menu option to reset to factory defaults, waited for it to finish and then turned the car off for 5 minutes. Started the car back up, put my flash drive into the 2nd USB port (nothing in first slot) and I got the brief indexing, indexing complete message and then the updating software message. Went for a fun drive (I love this car) and one hour later still "Updating Software". Pulled the flash drive and parked the car and haven't done anything with it since then.
I saw in another post someone suggested USB drives of less than 8GB and both of mine are significantly larger than that. I wonder if partitioning the USB drive with the primary partition being 4GB or something would help.