Ok, so in between everything else going on I've done a little more dis-assembly and sanding. Finally conceeded and pulled the sunroof out after looking at the dry rotted seal at the window, it's scrap. Going to pick up a new one this week. Got all the new seals and a new handle for the gate so all the parts are here.
Still can't believe how solid this thing is. I used a heat gun and pulled all the old seam sealer out and used a wire wheel to clean up the gutter. I'm hoping to primer tonight after a little more prep but I haven't added any filler or welded a single thing on this top!
I started to install the new self leveling seam sealer last night, SEM brand, works great I just didn't get enough. It should also be noted that if you pull all the old seam sealer out it will take 5 tubes at $35 each to put it back level with the top of the drip rail, oh yea and $60 for the gun. It's not cheap but it's the look I'm going for and will keep water from sitting in the rail so at this point I'm all-in. Another thing to note, this stuff really self levels, after spending 15 min trying to level up the gutters I got it about as good as possible. Problem is that the rail on the sides is sloped to the front and back around the b-pillar area. This caused some material (not much) to drip over the front corner. If I had to do it again I'd level the front and install that half and then level the back and install that half once the front cures enough (10-15 min).
I'm planning on getting the whole thing in primer and then painting the gasket surfaces and mounting surfaces with a black satin paint so it will match up with the liner. I may also add some duplicolor bed liner to the bottoms where it bolts to the bed and windshield. It's easily brushable and has a fine texture compared to the Raptor liner and will keep it from getting scratched up when it's off but still seal up with the new gaskets.