Ok, Ok another..........

The usual response to this type of question (although not really a direct answer) will be to go and get a professional fit at a LBS. While I agree that's the best way to make sure everything is adjusted properly, I think it would also be extremely helpful if someone could explain what you should be looking for when trying to fit your bike. I've been playing with my setup recently trying to get comfortable and I wish I knew the general geometry I should be shooting for. A site with some pictures of people on properly-fit bikes (tri-specific) would be great. I personally think that my seat needs to move forward more but it currently push as far as the rails will allow.

As for getting used to the aerobars...I think it took me 4-5 60+min rides to get rid of the sketchy feeling. You'll never have the kind of control you have on the hoods but I guess you learn to be comfortable and accept it.

Your best bet, by far, is to take the bike to a bike-shop and have them fit everything for you.  The cheaper method: stake out a 5 mile course, ride it, figure out what hurts, grap some tools, make some adjustments, and repeat until you're not sore.

This article gives the basics.
http://www.tri-ecoach.com/art20.htm