yes the TF doors are always a pain, but with all the pieces you've replaced it isn't at all suprising they don't fit well .... if you're real comfortable with the porta-power you might have some luck getting things closer, I un-tweaked one that'd been in a wreck, but it's real unusual to find one with good even gap all around .... the problem of good gap outside and wide inside is likely from the roof repairs, but also isn't uncommon
Bill