Let see if I can help you out Red383 all thou at first glance looking at your picture I may have let you down and didn't address the sail panel seam in the kind of detail the the area deserves. Ive been going thru my pictures trying to find some that might help you out the most, there are some in the thread but not detailed enough. I knew I would have to be able to slip the quarter on and off many times in order to deal with issues of fitment and undercoating and seam prep for welding and others reasons and believe me it was on and off many times but with the hinderences removed it popped on and off easily.
The first two issues to address that make a huge pain is the TAB and the reinforcing bracket in the quarter window jam. The Tab just cut it off flush with the rest of the seam, it doesn't serve much of a purpose and really gets in the way.
The bracket in the jam needs to come off while you install the quarter since you cannot lift the quarter over it for test fitting. Then tucked back inside the quarter and jam and welded back in place after the quarter is installed, this bracket prevents your quarter from cracking in that corner so its important to reinstall.
Now unfortunatley it appears from your picture you drilled and removed the portion or lip of the quarter that goes under the roof. If one was to try and slip the quarter under the roof the way the factory built the car it would be very difficult to get it underneath and if you managed it you wouldn't want to ever try to pull it back out. So the method I used which is also the same way the AMD installation centre does it is to cut the quarter off a bit below the seam leaving a small lip from the portion of the quarter that slides up under the roof. This provides a solid bit of backing for you to weld into when you weld the quarter back on but more importantly for fitting now when you slide the quarter on and off it just sits up against this up against this bit of steel level with the roof panel flange.
You need to grind the edge of the flange on your AMD panel or a bit of the roof edge so you have a decent gap so your weld will penetrate into that piece of flange the quarter is sitting against. This is a very strong area with backing so you can see I was able to dial up the welder a bit and make inch long welds cooling with air as I went and penetrating welds so this is stronger then the factory joint.
By removing the tab and bracket the quarter should slip on easily by first bringing it down over the window channel corner first, so from above and behind, then pulling the door jam and the back taillight panel in line should the need it to slide the quarter on.
I realize its a bit of work but I would be probably replace with a strip of steel that was the quarter panel flange that went under your roof skin and weld it back thru the holes that you drilled and just fill any other holes with mig wire. It doesn't have to be pretty but it would provide you with the lip for you quarter to sit against and to weld into. You can get away with quite a bit in this area since it will need a decent amount of filler or lead to fill the depression that this area always has.
If I can help with any other questions feel free to ask,
Dan