Hi again John,
After that sort of work is done on the body, it's entirely possible the number of pads and spacers need to be changed to re-align the frame and body. Removing and replacing panels such as the frame and rockers (especially the rockers) can change the shape of the body a little.
Did you use a lot of cross-bracing before removing things? I've not done it, but have often heard that when repairing IRS body panels it's best to have the body sitting on the frame and the frame supported by the car's suspension. Was that done? This is due to some tendency for the original frames to flex, more-so than the early "ladder" frames.
Do you recall the fit of the body before the car was disassembled so many years ago, or did you happen to take photos? If this misalignment was a pre-existing condition, I'd be more likely to suspect the frame needs work. If the fit was good before disassembly, then it's more likely problems with the work on the body or just alignment of the two that's needed.
A couple other things to check, body-related: look closely at the base of the the A- and B-posts. When floors and rockers rust out, there is also often damage at the base of the B-post in particular. It's often hidden behind the vinyl trim on the inside and the fender on the outside.
Yes, a 2nd, known/good frame would be an ideal test. Is there a Triumph club in your area with other folks doing restorations? Might be a good source of a loaner frame. Members of the club who are experienced with TRs also might be able to take a look at your car and spot the problem, too. They often work for beer and pizza!
Also, there are frame & body shops around my area that specialize in this sort of thing, perhaps in your area too. They are set up to take a bare or nearly bare frame and evaluate it against factory drawings and then do any necessary straightening and repair. Might be helpful.
It's not easy to check a frame at home on the typical garage floor and without some special tools such as a very long straightedge or laser alignment equipment. You need to find someone who is knowledgeable about older style cars, with separate frames, and not modern uni-body cars. Might be worth a little expense, just for the peace of mind knowing that your car has a sound foundation as a starting point.
One good thing... if really needed, there are brand-new, replacement frames available for TR6 and other IRS cars (not for my TR4). This is not cheap, of course, but replacment can be the ideal or only solution at times. Ratco is a frame supplier and advertises on BCF. Look for their links and check out their website, if you wish.
Before replacing, I'd try to get a pro to look over an existing frame and recommend whether it can be saved/used or not.
If you don't already have it, Roger William's "Restoring Triumph TR5, 250, 6" is a good book you might find helpful. He also has written "Improving TR5, 250 & 6" if you are interested in modifications and not concerned about originality.
Hope this helps.
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