Hannah,
Can't be of much help with the specific costs of your project.
Six years ago when I was having my Beneteau rigged, I attached all of the stays/shrouds while the crane held the mast in position. I just checked my invoice, the yard charged me $100. for one hour of crane time. I attached all of the stays / shrouds while the crane held the mast in position. Believe it or not, the yard did not charge me anything for restepping the mast. They charged me for 60 days for yard storage time and to offload the boat from a trailer and resplash. The total came to about $2000. Again, that was six years ago. Considering the length of time that you've had to pay to keep the boat in the yard, seems that they would give you somewhat of a break on the cost of the work that you are having done or at least a break on the cost of storage. After the boat was out of the yard, I paid an independent rigger to tune the rig including rechecking under sail, that really is the manner in which the rig should be tuned.... get the mast plumb, tension using Loos gauges, and recheck under sail. Approximate cost was $250.
Just for a price check, I would talk to a few independent riggers about the cost of installing a furler and tunning the rig to get some competive prices. This project is one that doesn't necessarily have to be done in the yard. Also check out their recommendations for furlers. Since you purchased your rig from US Spars, you can check on their recommendations for a furler as well as Beneteau in South Carolina. Another suggestion is to check and possibly negotiate a sale price at the upcoming Annapolis sail boat show next month. For reference purposes, my Beneteau 343 has a Pro Furl B35S furler; no problems to date. Not sure what furlers Beneteau is using now.