I just happen to have swapped my exhaust last week and have the extra gaskets I didn't use here next to me... the part number if you want to get some is 3GD-14613-00 and they were $8 and some change each. You're just asking for trouble in my opinion by trusting other people to work on your bike, especially other dealerships. Then again, if you don't have the ability to do it yourself or have friends that can help you there's not much choice I suppose.
As far as the Fi being worthless I'd have to disagree because even though the Fi2000 isn't as complete as a PCIII it at least offers some finer adjustments then just bumping the ECU and changing the mix across the whole spectrum. It's not like you paid the $300 that a PCIII would cost you so obviously you aren't expecting it to perform to that level of detail.
Good luck with the mods, hopefully you'll give installing them yourself a go and use it as a learning experience. The exhaust swap is pretty straightforward and the Fi install isn't too tough either once you know how to get to things.