well a deer literally ran into my car. luckily all i got was my quarter glass busted out, so i thought. turns out its not so easy to replace that glass. ive gotten frustrated. surely someone has removed there's before and can help! im desperate! its almost mustang week!!

 

Don't know if you're still stuck or not, but I just finished removing both of mine. Here's how i did it:
1. Remove Rear Seat & Seat back
2. Remove interior quarter trim (at the sides of the seat)
3. Loosen convertible well trim molding, I removed just 2 of the bolts on each side so it could be pulled away. Be Careful in doing this.....it will break if pulled too far!
4. Remove nuts holding the guide bar assembly. This sits in the well at the bottom of space the window assembly sits in.
5. Remove C-clip from regulator assembly.
6. Loosen bolts and remove inner window guide. Metal brackets sitting at top of opening w/ pcs of felt attached.
7. Loosen/remove as many bolts from the regulator assembly as you can get to. There's one in the back that I never could find/get to.
8. Now, you should be able to lift the entire window assemlbly up through the quater window opening. With most of the bolts retaining the reguluator assembly removed, you should be able to pry this inward to gain the clearance you need to remove the window assembly.

Good luck!