Mamma Shack,
Unless you have a long standing comforrtable relationship with the shop you are using, then yes - by all means do get another opinion (or two). Even if you do have that long standing relationship, a good second opinion and estimate is always a good way to keep your shop honest and even a way to feel more confident about your shop.
I do have concern about a shop feeling there is a $400 transmission repair? Gears get stuck? I would like to know more about that myself. I'm not sure what that implies.
The muffler...well..your exhaust will corrode as years go by. So that is not terribly out of line, from what I can tell.
Good luck!