I have a 2002 X5 but have only had a couple of the same problems as you:

A) the window regulators...had one replaced under warranty
B) the fast blinking blinker. it blinks fast when it is burnt out (either the bulb or the socket). I've had 4 bulbs and sockets replaced on mine over the last year.

Your warranty probably ran out so yes, they will charge you for fixing these items now. Not sure what BMW will do for you if you write a letter

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2002 X5 3.0 Sport Package, Premium, Cold Weather, Steel Gray w/ Black Leather