I am in the repaint the roof camp. Use the foil you have down as the masked edge. Paint it. Peel the foil and refoil it again. If you leave the flaw, it will disappoint you every time you look at it.
Did some detail painting of parts yesterday. Started into some assembly of the chassis and installed the dash in the tub. I have the 427 SOHC block painted. I will start on assembling it tomorrow.
Thin down your chosen color of paint to the consistency of Tamiya panel line paint. Use a frayed toothpick as a wick/brush and apply it to the center cap. This assumes of course the is a perimeter ridge like a Cragar S/S cap.
I admire your efforts. Your weathering looks pretty realistic. I went with the shiny new concept on my one and only diorama.
http://www.modelcarsmag.com/forums/topic/154551-grand-opening-of-the-american-restomod-workshop/
Nice project. Following. I just did a mini tub on a 67 Mustang. I too did not want to mess with the gas tank or the suspension too much. Spent more time on fine tuning the interior panels than the chassis.