Wanted to close off this thread as I've managed to solve both issues with all the help here.
1. Leaking from top of cabin
I couldn't find a source of the leak but removed the cover of the roof rack and removed the bolts. Propped up the rack a bit and applied liberal amounts of clear silicon. Appears to have solved the issue - no further leaking.
I think the roof rack was over tightened causing it to leak.
2. Drenched footwell.
As instructed above, got access to the drain tube. Tried to unblock it using a cable puller but couldn't get around the bend that must be in the firewall. Couldn't really easily locate the end of the tube under the car.
Blasted it with compressed air and a cockroach (well bits of) debris was found under the car so i guess this was the issue. Working fine now.
Note: Removing the plastic cover where the door lip meets the carpet was harder than I thought and broke some of the plastic lugs. That said, checking under the carpet - it was dry despite the footwell being flooded. As described above that plastic trim DOES need to be pulled down or the lugs will snap on the horizontal piece. Don't pull it directly off the bodywork.
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