Further to what you have mentioned..
1st to 2nd gear change can be a bit stiff when not warmed up, or if the gear change is rushed.
If it has sunroof's check them thoroughly as they leak like a leaky thing. (As do the alpine lights so check them too!)
If the water is getting to the rear floor, it is probably coming from the taped joint where the roof meets the join of the body and the rear corner panel. (I know what I mean... )
Check for corrosion on the inner front wings, the water/mud sits there and does it's best to make a hole in the wing.
Erm..... can't think of anything else at the moment.....
Mark