After reinstalling Android from stock images, why do updates complain about modified /system files?
Reverting back to original rom requires a full format as partitions as well as their attributes are usually different on different ROMs. This will solve your problem with the advent of a possible change in the device's info such as IMEI or similar. Another setback is the reduction in memory from formatting, especially if your partitions contained a lot of user data during the format.

Suggestion: repeat your steps again, but this time make sure to mount your /system partition and format it as well, unmount it after (it should automatically unmount).

Now. Let the flashing begin...