Hey,
With PTgui, you can delete control points from the list. I would delete all those with an error higher than 2 and try doing another round of optimization.
Then you can also output your pano in multi-layer mode, which will enable you to tune some possibly remaining issues by masked in photoshop.
But overall, I would indeed give CS5 and autopano pro a try.
Keep in mind that with film, you add possible scanning alignement and film flatness issues on top of the original capture issues. It makes it hard for advanced pano software because they tend to assume things. PS CS5 is a more generic blending engine and might do a better job this time around.
Cheers,
Bernard