Need help with 8.8 Swap

A few weeks ago I picked up a built rear end out of an 04 with 3.55's, Cobra diff, Moser 31 splines and bought a TA girldle to cover it. At the same time I picked up MM HD LCA's and a MM Panhard bar.

This past week I dropped it off at a shop to get it swapped and I got it back today. I pulled out onto the side road and thought I heard something making a noise, but it stopped almost immediately. I live about 2 miles from the shop and leaving a light about 90% of the way home I started hearing some grinding an pulled off onto a side street. Turns out that my calipers are making contact with the rotors on the outside. I babied it the remaining 1/4 mile back home and called the mechanic. Hoping he can come by tomorrow.

I'm not sure why, but both of the rear calipers are about 1/8-1/4 of an inch or so too far to the inside and are grinding on the outside of the caliper. I helped remove this rear out of the 04 GT it came off of and it didnt seem to have any issues. The only difference was that it was fitted with stock GT brakes. I have cobra brakes front and rear. The cobra brake brackets were also swapped off my stock 7.5 rear and put on the GT 8.8. If I remember correctly these should not relocate the calipers in or out only up to clear the bigger rotors.

Anyone have any ideas on why i'm having this clearance issue? I took it apart and I'm not seeing anything blatently obvious. I pulled rotors as the mechanic already agreed to turn / replace if necessary.

2000 3.8L 5-speed Mustang
Non ABS, no trac control
Mods listed below.

Rear came out of:
2004 4.6L 5-Speed Mustang GT
ABS and trac control.
 
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