Not too bad, comparing your transaction with shops around here.
Local shop hour rate around $ 100.
Double taxation definitely should be adjusted.
High-sided somewhat on the tire and tube purchase.
Now, all this said; I'd recommend: Negotiate and agree on prices for parts and labor BEFOREHAND. Oh, a few jokers in the deck might appear even after that agreement, "Disposal Fees," etc. When buying tires and paying for installation and balancing, you might shop around for best prices; find out the difference between wheels unmounted and on the bike, etc.
I was hosed by an independent Harley chop-shop myself on tire changing (I trusted them, did NOT get a price in advance, my mistake). Also, tubes do not necessarily need to be replaced with new tires, IMHO; YMMV. (BTW, KLR rims (stock) DO require tubes, whether tubed or tubeless casings are used.)
Aside from correcting the double-taxation clerical error, don't think you have much recourse. They've got more, and you've got less. Chalk it up to experience, and tuition for reality university!