Need some more bike advice

Sounds to me like the online deal is too good to pass up.  You can always find a sympathetic friend in a local bike club who might be willing to help with bike adjustments if needed.  Not sure what shop you're going to in MA, but possibly you could find one different from the shop you are now dealing with for any adjustments you couldn't handle.  I can't imagine that a tuneup would be prohibitively expensive. 

The main difference between 105 and Ultegra is the weight; Ultegra is lighter.  They are both excellent and reliable components systems. 

The bike, which you are referring to, that you can get online for $550 less than the one at the bike is four years old (the 2005 models are out already).  It will have four seasons of use on it, so will definitely not be a new bike.  As has been mentioned already, if you buy online you will have to wet the bike up to your specifications and maybe change a few parts that are worn or damaged.  As for shopping online, the old axiom "let the buyer beware" applies most aptly, so be forwarned.

Got to disagree slightly with Mach here, the Ultegra adds a lot more precision in their shifting than the 105. Ultegra is engineered to the same specs as Dura Ace components, just utilizes different materials, so you could say "The main difference between Dura Ace and Ultegra is the weight."

Not to say that 105 isn't a decent level of componentry, certainly miles above Sora/Tiagra that you find on many entry-level bikes.

Will agree with him that the online bike is a used bike, you have no way of knowing with certainty how much or hard it was used over four years, and it won't have any kind of warranty as will a new bike.