Finally got it working again after a lot of mucking about, some how the flashpaq had been temporarily disabled by the update program, at least that was the error that kept coming up when I could eventually reconnect to it.
had to reboot the computer, uninstall the update program, rebooted the computer, reinstalled the update program, logged back in & connected the flashpaq, flashpaq connected & upgraded with out any more issues, all good now, looks like the new upgrade is finicky how its run.
make sure you dont have any other programs running in the back ground when you upgrade firmware & I think you should be ok
The only thing I could find on the can port time out error was on firewall & security issues, in this case that wasn't the issue
Went out & reprogrammed the Jeep with the new firmware program, all good