On the MPEM, which fuse is blowing, MPEM 5A or BATT 15A? If MPEM 5A I don't think unplugging the rectifier should make any difference, the MPEM 5A fuse will still blow if the MPEM has the infamous shorted surge protector diode in it is bad There's a pretty good sticky on the forum about MPEM troubleshooting, it has the info on the diode I think.
If the stator or rectifier are bad, the BATT 15A fuse will blow.
So based on what you said, it sounds like a bad MPEM, but it doesn't make sense that unpluging the rectifier stops the fuse from blowing, so please double check your work and confirm?