An intelligent reply and plan will only come after you get the entire pad off to see whether that impressive rot and rust is contained to only the area of the apparent chronic water leaking.
If you still have the finish paint and clearcoat at every other part of the roof, you MAY consider splicing in a patch after removing that sunroof. I would only use the most experienced and trusted shop to assure an invisible patch. Then you only have to attend the other parts of going vinyl-delete = backglass, path 20 holes and resmooth the sail panel ditches. And a new headliner.
\'96SS SOB: SSRI, Herter Tune, Tri-Y II, , 3000 Edge, F/HO bars, METCO extendeds with CV MMC, Bilsteins, currently Vredestein Ultrac Sessanta (315/35 rear). Finally, wait for it... LT-4 knock module!
\'96FWB BUW-Butt Ugly White: PCMPerformance tune, HDFA w/ swissed filter, 1/2 SLP s.s. catback with H- and Flow Super 50s, oem opti rebuilt 3 times, SS Bars, METCO LCA, Airlift 1000, Monroe SS, PowerTrax No-Slip, CTS wheels with +1 rubber. Finally, yes again... LT-4 knock module!