[Charles Freeborn]

I second the motion to get it onto a frame machine of a shop that really knows Porsche and see what's going on. If all the alignment specs are within tolerance you may look to do adjustments elsewhere. When you say the roof opening do you mean where the Targa top meets the top of windshield / targa bar and or tops of windows? Targa tops are notoriously inaccurate and your solution may be to re-work the targa top first. Window mechanisms are adjustable too.
Metal fatigue is questionable. Steel is not prone to it, as aluminum is. Use the search and you'll find a write up about fatigue (or lack of) and torsion bars. If the car has suffered a trauma ( accident, elephant sitting on it, etc) then you have other fish to fry.
The tub of a Porsche (or any car for that matter) is a rather scientifically assembled thing - i.e. sequence of welding to counteract the warping effects, so going in willy nilly adding plates here and there could cause more problems than you've already got.

Pretty car, by the way. Mine was that color originally, and will be again one day.

-C