I need your advice please.

I bought my Traveller in the summer.
The woodwork is approx. 5yrs old & sound.
I've done quite a lot of work on the car, inc. a new rear Headlining & new under felt.
Although covered when at home, I do drive it very regularly & in all weathers.
The rear passenger foot area is a squelchy paddling pool..!

The cab-roof T-rubber does not seat too well at the ends so I have used some sealant as I did not know that
the Headlinings need parting to fit a new T-rubber...I'll tackle that job if I really have too later.
My thought is that it is unreasonably wet in the car for a slightly dodgy T-rubber.
Even the box "cross section" under the rear seat has water in it that does not appear to have tracked in via the cab-roof join.
Is there some other known point of water ingress that I do not know of?
When I renewed the under felt, I plugged up all the unused holes in the floor pan with grommets.
My Traveller is proving fantastic fun & ultra reliable but this persistent problem is very frustrating!
Any advice will be gratefully received!
Andy.