I love to do things myself. But the line is drawn here with me. Over the past year, I have watched the slow, difficult and expensive steps taken by an experienced Healy body man required to bring the doors and body panels into proper fit and alignment on my 66 BJ8. While not black magic, this stuff is complicated. Every step you take in one area affects the entire car, it seems. I've been through what Robert is experiencing. Not fun. Good news is that the result is fantastic.

One thing that comes to mind as a possibility. When the sill was removed, the lower structural support for the hinge pillar (which is welded to the outer side panel) would be gone. The pedal box brace would hold it in position somewhat, but there could have been some sag to the hinge pillar that wasn’t addressed when welding the sill back in. An eighth of an inch sag at the pillar would equate to a much larger degree of off-ed-ness at the rear door-to-shut pillar. An additional thing to check is how the aluminum finisher fits along the rocker and sill. While it rests on the rocker, how does it fit the sill? I would venture a guess that it will be too short at the back. The double fold that overhangs the sill will not reach over the sill and still be resting on the rocker panel. The arrow in this photo shows the direction that the hinge pillar would have sagged.

Robert,
I feel your pain with this issue. I have a 63 BJ7 #20040. I have been doing a frame off restoration the past 6 years. I have been in your exact same boat. I replaced inner and outer sills, floor pans, big rusty areas in the tops of frame rails and 2/3 of all the rea inner sheet metal. I made the mistake of removing the rear inner sheet metal from off of the car.
What I would do is make sure that your frame is level underneath. Look in the book or th back of the Haynes manual for dimensions. My frame was like an old sway back horse and I had to bend the rear 3 ft or so back down a slight bit. That should make your shroud come down at the top. I had as much overlap as you have. Also, like others have said, just a little change around the sill can make a big difference in the doors. I had cut and re-welded my inner panels so many times that I had to get a couple new ones because the the first replacement set was too garfed up. I had the doors off and on propbably 100 times or so. I too had not enough clearance like you.
Eventually, things came together, you just need to keep after it. I actually started at my front fender where the car dimensions were all original and no panels were replaced the got the front door gaps to fit well, shimmed ones side slightly, then worked on the rear door gap. I moved the new rear latch panel (B panel or post) to the back of the car 1/8 or a 1/4 of an inch. I actually had to grind about 1/8-3/16 off of the front of the shroud to get it to fit behind the little chrome finisher.

If I had it to do over, once I had my panels on (which always move when you weld them anyway unless you have them clamped in a jig). I would take the frame to a body shop, all wheels on the floor or at lease jack stands at the wheel points, then clamp the frame to the floor and use a portable hydraulic puller to get the dimensions correct. Then split the difference between the panels. I had to make holes bigger and really move stuff around but now my car is painted and my gaps look really good. All of the hard work is worth it in the end.
You could put the hydraulic ram, (I think that Harbor Freight sells them for $150 or so) inside of the car and brace it against the corners or the flooring, use a piece of wood to spread out the preassure of the ram, then push your sill out slightly if it needs it. You might get 1/8 to 1/4 of an inch doing this, I did.
As far as your doors being cut too much if they are, you can always get some 1/8 square stock at you local hardware store and tack weld it back on then grind to fit. I would finish it up with one of those all-metal type body fillers though. They tend to be stronger than typical polyester body fillers.
Note: If you jack your car up at the ends of the frame, beyond the wheels, especially at the rear, the door gaps can change as much as 1/4 of an inch at the top.

Randy
Healey-Archaeologist
63 BJ7
66 Cobra replica
06 Mini Cooper S