I'm almost sure that the low spots came from heat we he welded the seam together. I would try a stud gun and see if you can pull the low spots out instead of cutting open and then tring to reweld and maybe have the same results. Also 3/16 is not all that bad, I can tell you on the collision end there are alot of guys that would love to only have 3/16 inch of filler in their work

. Also when you use the qtr skins you lose the curve of the panel from the top going down so you may need that much fill to make it look correct. As for you roof if yours looks like what mine did that rust will come back FOR SURE. Those vinyl tops are a killer on metal. I would just replace the roof panel they do not cost much (I think under $400) and are very easy to change and can be done with very little experience. I can and others can walk you through how to change it. Hope some of this helps.