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Re: water ingress
The pollen filter ususally figures when its old and blocked, if you've just changed it, that's not going to be your problem.
You could check the bulkhead drains, make sure they're not blocked.
It's more likely to be the sun roof drains. The holes are more or less in the front corner of the sun roof, connected by a pipe to drain from the back of the front wheel arches.
I had the same issue, it proved to be the drains were blocked at the wheel arches. Resolved by unscrewing the plastic inner arch cover sufficiently to prise it out and get behind it. Then scraping away as much of the mud caked behind as possible, for both sides.
Just to make sure, I bought some heavy guage strimmer cord and poked it down the drain holes. The strimmer cord is plastic and unlikely to tear the drainage tubing.