I am not familiar with HD dealers; can I hand them an Arlen Ness Big Sucker Air Cleaner and a set of Cycle Shack Slip Ons, and say install these and remap (or will they only install what they sell)?
That really depends on the individual dealer, but generally speaking, they're usually not to happy about installing customer supplied parts that they don't get their 150%+ markup on. They're likely to sock you on the labor, which is already more expensive than an indy.
Order the A/C and slip-on's on-line not through the dealer.
You haven't filled out the "Location" info in your Profile so I don't know where you live, but it's usually not hard to find a decent indy unless you live in Po-dunk.