0541 don't worry about it... you can override it by reconnecting the black wire since that code picks up the absence of a ground.
0340 I wouldn't worry about either. Just get a spare CPS and put it in the glove box. It's easy to fix and usually with a CPS issue you can nurse the truck several miles if need be. Plus it's a finicky sensor anyway...
1105 At least you knew which alternator to test. You could get by with that one faulting if you had to b/c of your dual setup, however if you're like me you want everything to be functional.
As far as the other one, I don't know - looks like scuffy already told you about that one.