Not sure about Ford, but I looked at a factory Honda sunroof. They put drain tubes in there that go down the windshield pillars and out down below.
I don't think an aftermarket roof can do that. So, where, pray tell, does the water go that is in the track etc.?
I worked with a guy who was on the desk for Nissan warranty claims, quite a while back, but anyway he spent a lot of time explaining to furious callers about how the dealer-installed sunroof was not warrantied by Nissan, sorry you are having so much trouble, call the dealer who sold it to you, you already did....sorry..... and so on.
NOT worth the risk, imo.