Well when you restore everything is wiped. You have the option to use a backup from the last time you syned but i chose not to since the last backup will be from when you were jailbroken. I think the backup will only put the non-jailbroken stuff back on the phone but i wanted to start from scratch.
I jailbroke my 3gs on Monday morning and have not experienced any of the problems you are talking about other than the battery meter was flashing back and forth but that only did it once or twice. my battery is drained just as much as it always is. you have to remember these iPhones are always busy working so it will drain the battery. I repair iPhones and sell them and have several that I have charged and the battery will stay up for several days with no sim card in them.
I really don't know. The apps took longer to load and icons took longer to load on screen when i clicked home, i also had a crap battery life and a eratic battery meter like others have complained about. Im back on stock firmware and things are nice and fast now