Well, I replaced the seal on the AC cover. Time will tell.
I took the cover off. Removed 3 layers of various gaskets and sealants from BOTH surfaces so I was down to bare fiberglass and cleaned the surfaces very well.
Some of the old well nuts pulled out, some I had to cut off the rubber tops and let the bottoms fall into the roof cavity.
I was able to get a set of 12 well nuts with stainless screws from Amazon for about $15. I only needed 9. I had to cut 3 of the screws a little shorter for the 3 front facing cover screws. They would bottom out against the internal case of the air conditioner.
I used two layers of 1" X 1/16" closed cell foam sticky backed tape on each surface.
You can see from the pics below, that someone before me cut up some foam pads and out them on the top of the AC. I suspect to keep the cover from sagging. It didn't work very well. See the pic with the level. If you look under the level, you can see where the "dips" are where the cover fastens to the roof. Also, the deformed sag in the cover overall. Another pic shoes the cover with one side layer of the black sealing tape. The other pic just shows the completed cover attached.
This is an absolutely HORRIBLE design. There has to be a better way.
We've had significant rain in the last 3 weeks, and so far, no leaks. That said, I haven't parked nose down either, only level, but the van sits a bit high in the back anyway.
Time will tell.