Ok, when you change the exhaust from stock to a full aftermarket, you eliminate the servo. On a lot of bikes, they measure resistance internally, and will throw an FI code if they do not see the servo. There is an aftermarket adapter for this elimination of the servo, and it usually runs around $100-$150, depending on who you buy it from. Additionally, they probably are planning to make you pay for replacing the rear set that they broke, plus shop labor. All of that would probably be about $400.

My suggestion - buy aftermarket rearsets - look for Vortex or Woodcraft - preferably a used set on Ebay. Those should run you $150-200 for a pair in like new shape. Buy the servo eliminator, do a search on Google for which is the best for your bike. Get the full Two Brothers twin exhaust, and a PC3. Put all of that on yourself (it's easy), and then take it to get it tuned immediately.