Post the full log. Every Hyperterminal capture I see from a player booting seems to get totally munged and missing characters so that "half" error might be due to that.

Post the whole log and if you can get something like TeraTerm or CRT use it instead.

You can also try the upgrade again. It can't hurt doing it twice or even 100 times.

Edit:
4 hours is very long for an upgrade. A dodgy drive could esaily slow down the pump process. It takes a while but maybe 10-15 minutes and not 4 hours.