The sunroof requires a teflon infused grease, usually webasto sell it and so do mercedes benz, but pricey.
Japanese manufacturers say to slather white lithium on it which makes a very bad mess.
The greasing is done by first cleaning evrrything and then and extremely thin coat is applied.
The water drains actually have reed valves in them where the are mounted to the car, so road noise doesnt travel upwards from it.
The sunroof is not 100% sealed. Its a controlled water leak so a monthly check regime of the drains is required.
You have done a big job, but the correct book way is easy to do too, the roof panel is glued in place then spot welded with a tig. This way the structural stregnth of the shell is not compromised.
This is unibody design and the pillars and roof are part of the chassis.