Sounds like an error on their end, then. :( Likelihood of buying properly sexed pullets from a correctly labeled pullet bin and getting that many boys is really low (10% mis-sexing is the norm). Sorry that happened to you, but glad you have options for getting new birds, and unloading the boys.
Did you buy straight run? Or is this a case of TSC mislabeling a bin? That's pretty discouraging to have to deal with right at the start of building up a flock.
Vacant for a year is even better!
And yes I'd mask up for sure - when cleaning my coop I wear old clothes slated for the garbage and tuck in the shirt, tuck pants into boots, plus a mask, goggles, shower cap over hair and ears. It's amazing how much dust and dander accumulates in a coop.
Since it's been unused for 6 months I'd honestly just go for a surface clean - broom, paint scraper & shop vac (or blower), getting out as much old bedding, poop, etc as possible.
A dry clean is my preference, no worries about waiting for things to dry out, and since it's been quite a while...