OK
I have a 69 camaro on a rotissory that was sand blasted and epoxy primered, at that point I found the car, since then I've purched new fenders, hood, grill, replaced 1 full quarter and partical floor and part of the other quarter, very lite dings on doors that I've been working on, the car was origanaly a vinal top, it has pitting around the out surface edges that was sand blasted with a couple of small holes blasted through in 1 spot. I welded them as well as the mounting clip holes. The center area of the roof has less rust however seems that it was not sand blasted as the very lite specal rust as well as 4 or 5 areas the size of a quarter has shown through after sanding, If you run your hand along the surface you can feel warping, so I sprayed the roof with some gloss black spray paint you can see warping around where the suports sit under the roof, there is also a dint on the surface the size of a foot ball (where there is no under supports)that you can pop back out but wont stay, its hard to see but you can feel real easy, what to do for this is my question, how to neutralize the small amount of rust and fix a surface that dose so much flexing when any amount of pressure is applied.

you are going to need a Body man that know how to shrink the metal on the roof, that is an art itself !!!

I bet that roof was warped from the sand blasting getting it too hot.

If you're looking at replacing anyway.... try the heat trick. But do NOT over heat or use a torch, instead use some heatlamps or heat gun.
No glowing hot, just to about 140 or so (thats about just hot enough to not touch)

Just a thought....are you going to reinstall the vinyl top? Would it cover the imprefections? As far as the dent goes perhaps when you glue the vinyl top back to the roof panel it will provide enought support to keep the dent from flexing.
Maybe you could install some sort of inner bracing to support this?

Just thinking! :D