Hi Holytouch:
Q1 - Maybe this thread might help:
http://986forum.com/forums/showthread.php?t=7008. Look for MNBoxster's post on 'standardizing' the side windows. Supposedly this in the manual you don't have.
Q2 - Don't know. I've read on renntech.org, here and/or
www.ppbb.com people having problems with electrical contacts. Or, it might be that the remote needs to be re-programmed by the dealer. Or, maybe you need a new remote from the dealer. I understand the last option is a pretty pricey.