Teach me to remember to go to page 2 before posting...
Problem 1:
From your log are you referring to the entries at "090807 14:10:40"? It looks like there was already a mysql server started when the one from this log tried to start, make absolutely sure that all processes from the zimbra user are killed before attempting to run any backup/upgrade/install.
Problem 2:
Never messed around with this myself but I believe
[SOLVED] Law Enforcement (aka intercept)? is what you are looking for, since all IM conversations are sent as emails to the participating users, this should grab them.
Problem 3:
clamav updates it's database periodically, no interaction required
