Sound slike an alright car if a little over priced (unless it's really good nick apart from the mentioned flaws.

the door seal you mention mate, my S1 hasnt got this seal (needing to be fitted, jus not got round to it) and after a year and a half its not leaked into the passenger footwell. it'll be the battery tray or the sunroof, ask the boy if its ok to take the glove box out (2 screws iirc) just to double check.

the gearbox problems could be sorted with an uprated bernie box, or if it's can be sorted to bring the boost in a little more gradually, or maybe even the boost turned down wouldnt let the box problem put you off though.