So I'm running with Tim Bradley (thanks for the recommendation Rodney!) and he came in a bit lower than everyone else, but most importantly to me, has been around since 1918 and seems very reputable. He's the 3rd generation owner, a local fellow and they're located close to me so I know where to find them if it starts leaking again.

They're installing a EPDM membrane commercial style flat roof on the rear of the house to replace the V5 metal panels that shouldn't have ever been installed.
As far as the rest of the home, he's letting me select whatever type of shingles and was wondering if anyone had any recommendations on what to run with? He was also the only one to email me pics of the findings and volunteer to replace the archaic silo style attic vent in lieu of something more modern.
Man, I must have spend 10 hours researching this and have to say I'm really disappointed in Baker as I wanted to give them my business since they sponsor local cycling and I hear their ads on ESPN radio. The tech came out, never followed up so I submitted my info again hoping for a call back and still no response. Business must be good...
Buzzard was super nice too and they'd be a close second.
My only advice is that it's worth getting many quotes because the pricepoints can be all over the board.
-Matt