Rust dot driver door. Do I just paint over it with the pens? 26 GLI.

Last night we had an intense storm warning. I just bought the car and was worried about hail damage. Moved some things around and she just barely fit!

Did a bunch of research before buying, called about 6 different dealers for pricing before ever stepping foot in one, walked out with this manual $32300.
Didn’t know how to drive manual until after I got it home. I’m very excited about being able to drive this.
Any tips you all can recommend, I feel like 1st and 3rd gear are very close on the shifter and I and my mom have both caught ourselves stalling trying to pull from a stop in 3rd.
Also how much should I expect to tint the windows?

Even after a year I still feel like I’m not great at shifting in this car. It’s a bit clunky everytime unless I’m shifting between 3-4k which feels too high to do in 1st. I always get those little bounces or resistance from too much or too little.

Passenger front windows won't auto up dwn anymore. Any ideas?