We have just had both our sunroofs out and resealed them to the roof, rubber seals were renewed last autumn.
The leakage was not where we expected at all, it was from the screws that hold the two halves of the sunroof together. If you park uphill, with the drain tubes at the front, any water getting into the drain tray goes above the level of the upper/lower parts joint and leaks through the joint into the headlining and into the car.
All four drain tubes and corner pieces were fine.
Go to B&Q, look in the plumbing section for "Drain Valve Washers", they are just over 1/2" diameter and 1.5mm thick, £0.98 for a 4-pack. You need 14 for each sunroof. Once you have sealed the sunroof and fitted those washers under the heads of the screws, you should be pretty dry.
THEN, you can get your carpets up and dry them out.
Our back carpet was so wet that it ran out of the foam underlay when we hung it up to dry, we had to put a bucket under the corner.
The other area of leakage was the roof bar mountings, which although they had foam round the base, it wasn't compressed and actually had water right across the face. We removed a single washer from under each mounting and ran a ring of sealer around the roof hole before bolting them down again. The foam now compresses and the sealer should stop any liquid getting through. The rear mounts have a 3mm thick washer which must stay in place.
No water coming in at all now, we had rain last night, all is dry.
Both Alpine and side windows show no signs of water ingress,
The floor is absolutely pristine and unrusted, the fuel pump access planel was rotten rusty, obviously not painted or prepared the same as the body. We'll buy a new one plus the rubber seal.
Peter