$2800 to fix a manual trans, that's nucking futz, check out the trans guy on the right, chances are it'll be alot less.
As for whether or not to trade the WS6 on the SS, it's basically the same car, other than the the sheet metal (a few minor differences in trim and interior appointments) all depends on what body style you like better, personally I like the WS6 better than the SS, so that's what I bought