To clarify, Indian sells their "Performance Air Intake" filter for $104.99 and it comes with a flash card. That flash card gives them two options for programming. Stage 1 or Stage 2.
I opened up my exhaust with J&P Slip'ons so they did Stage 1 for me. Programming your bike with the flash card is a separate cost and takes just a few minutes. My dealer was cool and only charged me 15 min of labor (probably because I'm a beer homebrewer and give my buddies that work there free beer all the time), but could have charged a standard full hour rate if they wanted.
What's really stupid is if you try to buy just the flash card itself it costs somethin like $125 and you still have to pay labor costs for the flash job, so if you had your own air-intake that you've already installed and only wanted a Stage 1 flashing (as opposed to actually tuning your bike) you can acquire a flash card more affordably by buying their performance air intake filter since it comes with the flash card...... and then just.... toss the filter I guess..... A pointless waste if you ask me. I don't know who decides product costs at Polaris, but whoever they are, they need to back off the energy drinks.
I believe the reason your cost was so high is because they're charging you for the filter, the labor to install the entire filter housing (which involves dissembling the side frames), and the seperate labor cost to flash (or tune your bike if that's what you're actually doing). Add taxes and there you go.
Honestly, installing a filter yourself is not that hard, you can find YouTube videos on it, and if you're using Indian's Performance Air Intake filter, you don't have to remove the entire filter housing because it's the same housing as the stock one, just remove the gas tank (ONLY the gas tank, leave everything else intact) and remove the 6 screws that hold the filter to its housing.