03 and 04 GT need help!
 

Alright, here's the deal.

2003 Mustang GT is totaled out, I bought back from Insurance.
2004 Mustang GT is a rolling shell no engine, trans, interior.
Just the suspension, front and rear end, and that kinda stuff.

Here's the thing. The 2003 is a 4.6L Automatic. The 2004 was a factory 4.6L 5 speed. Now, my question is... Will my transmission/driveshaft bolt up fine without any problem??

I mean I get the angle of the driveshaft has to be at a certain angle, etc but as far as the mounting and what not of the trans, should it bolt up just fine? I mean obviously they both have 8.8 Rear Ends, the whole Track-Lok setup and what not just alike...

I'm doing a complete swap from one car to the other.

Any help and or advice is appreciated!

I doubt you will have much problem. It doesn't benefit the car companies to make different shells for an auto or manual during the assembly process. Each shell would be stamped with bolt holes, etc for an auto, manual, gt, v6 or convertible.
The only issue may be the fitment of the interior bezel for the shifter, but since you have those parts, don't forget to swap those as well

Should be no problem since you're swapping everything out. That should include wiring harnesses and ECU. But there's no difference in the basic shell of the car like Steel Pony said...