Where to being with this, I recently bought my Mk3 VRS used (but new to me) from a good friend. The car has a pano-roof, which i wasn't massively fussed about and on the basis of my experiences so far I will never buy a car with again. Long story short within a few days of buying the car i found the roof was leaking. The issued appears to have been fixed now by my local VW independent specialist who had to remove the roof, fit a new seal, re-bond the roof to the plastic frame and then refit.
As a result of my issues I've done a LOT of research into these roofs the last few weeks so prepare for a long winded response.
The roofs themselves appear to be manufactured by Webasto however the VAG appear to have a particularly poor track record in terms of leaks and drainage issues when compared to other marques.
Clearing Drainage Tubes
The most common issues are the sunroof drains themselves becoming clogged and flooding. The way to test this is to carefully run some water into the sunroof tray (i used a squeezy mineral water bottle) and see if it drains effectively - the drain points are at the front and rear wheel arches. Even if still draining okay i would suggest this should be a yearly job. My front drains were nowhere near as efficient as the rear drains.
With the roof open, the drainage points can be found in the four corners of the plastic sunroof tray, however the two rears ones are not readily visible and are hidden by the mechanisms. The two front ones are easily identifiable and are circular holes a few millimetres in diameter. These drain points are bonded to drain tubes - I've seen other people have these bonds fail and leak or become disconnected and they have had to drop the headliner and re-bond the pipes to the roof.
The front drainage tubes run down the A-Pillar and exit at the bulkhead in the engine bay. The drain tubes themselves are just push fit into a rubber boot at the bulkhead and again in mu opinion there is the potential for this to work loose and leak.
The procedure i used to clear the front drains was firstly to open the bonnet and remove the rubber stripping from the plenum chamber cover - it will just pull off. From there you will see there are several metal clips which secure the plenum cover, again these will pull out and you should be able to lift both corners of the plastic plenum chamber cover. The workshop manual suggests the windscreen wipers need removing, but even with my shovel hands i was able to reach in under the plenum chamber cover and feel towards the base of the A-Pillar where you will feel a rubber nipple. You need to manipulate this and you should feel an amount of gunk work clear from the nipples, this in itself should improve the efficiency of the drainage tubes markedly.
To clear the tubes themselves some recommend blowing compressed air from the drain point in the roof tray, however VW seem to advise against this and the workshop manuals refer to using a bowden cable or similar as a drain snake. Personally i wouldn't use anything metal or too rigid as the drain pipes themselves aren't especially heavy duty and i could see the potential to cause damage.
I purchased some plastic garden strimmer line for a couple of quid from the DIY shop - 2mm diameter, in reality i could probably have done with using the same stuff but a bit thicker as this was a bit too malleable and not strong enough. As such i doubled it up and taped it at several points to double its thickness and make it a bit stronger. It was then a case of gently feeding it down the two drainage pipes - if you hit any snags its probably a bit of blockage, working the cable back an forth it should push through and i was eventually able to get my cable to appear out of the bulkhead nipple and then basically 'flossed' the drainage tube. I repeated this several times and quite a bit of gunk was loosened. I then repeated this on the other side front drain.
Finally i used a large syringe containing hot (but not too hot) water and washing up liquid and injected this directly into the drain point just to try and degrease and clean any final bits out.
As discussed the rear drainage tubes cant be easily accessed from the top by my eyes. The workshop manual suggests these exit by the rear wheel arch and that access to clear the drain point nipple can only be gained by removing the rear bumper - which looks a right ball ache. I have seen some suggests that taking off the wheel and arch liner should also get you access. You could also clear the tube from within the car - removing it from the rubber boot where it enters the drainage nipple and exits the car, but this would mean removing a lot of the boot trim. This was all a bit involved for me as my rear drains seemed okay, however i will keep an eye on this. My research suggests that the way to clean these drains is again using your improvised drain snake - however this time from the bottom up, feeding it from the wheel arch nipple up towards the roof where it should emerge.
I will stick another post on shortly re: the lubrication of the mechanism and seals