1. The center arm rest, as far as I can recall, only opens partially. I don’t think it opens to a full 90 degrees… With that said, it should open enough that you can get a screw driver in there to reach those two screws holding the lid on. What likely has happened is the hinges broke, since most people put their weight on it to shift their body when in the car… They’re very fragile hinges.
2. Have you checked the spark plugs, air filter, etc? Cleaning MAF on these cars doesn’t do much, really. Cleaning the TB does help though. The shuddering has probably disappeared since you disconnected the battery to do these, and the car is relearning it’s idle. Give it some time. If it starts happening again, try to pull the codes. It may have pending codes that haven’t caused the MIL on the dash to illuminate.
3. That is a good question… I need to address the weather stripping on my ’04 GT. Quick search brings me to this which gives a breakdown on how they replaced it… Would be similar on your second gen vibe. viewtopic.php?t=45951
Not sure if a source for the seals... Quick google search suggests eBay or stealership.
4. I would take an air compressor and blow out the sunroof drains. I don’t know about the second gens, but the first gens are prone to plugging up… You’ll then take a turn and look like you peed yourself.
Outside of that, there isn’t too much to worry about on the sunroof.
Not to detract from our grand website, but if you’re on FB, come join us there too. www.facebook.com/groups/Genvibe
Nothing will ever beat this site, but we do use FB to the extent (not that great) that we can for a forum.
PS: You get brownie points for adding pictures to your introductory post you made.. More brownie points if you add general location so we can try to link with other members in your area if need be.