1 - Yes
2 - Yes
3 - Yes it does, if you are using a huge VGA then put a bit of tape on the one bit that might touch the card. (certain noctua coolers only)
4 - Go have a look over on TonyMac's forum. He has a list of suggested builds and graphic cards.
To help us help you - please provide as much information about your system and the problem as possible.