I just called my dear to get some price quotes, and the lady in the parts department told me all '06s had to be ran on the dyno to have the carbs adjusted. She quoted me the prices:
Carb kit $139.95
Dyno/download $150
Labor (3.4 hours) $268.60

Totaling $558.55 and that does not include new mufflers or an A/C.

I was thinking about some Screamin' Eagle or Cycle Shack mufflers, and the HurricaneFlow A/C. I may just settle for the new mufflers and old off on the carb work for now.

nharp

WAY too much!

There's no reason why the '06s HAVE to be run on the dyno. That sounds like a load of crap from someone who doesn't know.

Also, you don't need a $140 carb kit. I got more carb kit than I needed and spent $100 on it, retail from the dealer.

My FULL stage one (SEII Mufflers, SE A/C, and carb kit) cost $600 from the dealer. I ended up getting it dyno'd later because of carb farts. The did a couple pulls and changed the slow jet, charged me 1 hour labor (@ $60 - no charge for the jet).

You'll need to do the carb work if you change the AC and pipes. Check the threads though, there's plenty of advice for a good starting point for jets (you don't need the rest of the stuff in the kit, generally a $15 slow jet does the trick). I don't do my own carb work as it makes me nervous, but the pipes and AC are easy to put on, could easily do it yourself.

Spend fifty bucks on the shop manual, then buy pipes, high flow air cleaner and a jet and do yourself. You can do all of it for that price. I was worried about the carb myself but re-jetting is really easy.
There are plenty of pipes or slip-ons to choose from and different air cleaners also. Check out the archives and decide what is in your budget and buy them. Anything will give you improvement over stock.
If you just want to let it breath then Cycle Shack pipes are a good deal and easy to install. Air Cleaners, there are many different opions on that.

I have the Cycle Shack (baloney cut) pipes, not slip-ons, Screaming Eagle A/C and a .45 jet.
Looks like you are just looking to do a stamdard stage one and don't plan on runnimg it on the strip. Good luck and I am sure others will have suggestions.
$600 is just tooooooo much to spend and not have pipes and A/C

That is outrageous. $558 is what you should be paying for the whole stage 1. Get the manual, read the "Jetting 101" post and walk away with more money and more pride in you machine. If you run into any snags, you've got a few thousand people here who answer tech questions within about 5 minutes. I was a little sketchy about doing carb work myself- until I tried it. Follow directions and take your time. Anyone with basic hand tools and very basic mechanical skills can do this.

Cheers,

Luke

my alternate to the dyno was to carry a screwdriver with me for a few weeks' worth of riding. I would change the mixture and see how she did, if was worse, I'd change it back. It worked. I have a ramflo and I punched out the baffles on some 2nd hand stocker muffs, seriously carb work is not at all difficult unless you have no thumbs...

The local dealer here dyno tuned my bike for $100. I had the 49 state slip-ons. SE air cleaner and jetted from the original dealer when I bought the bike, 45 slow, 165 main jet and the air mixture screw out 1 3/4 turn. When they dyno tuned it all they had to change was the main jet to a 175, which was an extra $6.00. I've sinced changed the pipes out to Supertrapp 2:1. I get some carb farts when cold and I've pushed in the choke too soon. Other than that the bike runs pretty darn good. I'm waiting on my Ramflo 400 to arrive. When it does I may need to do a little fine tuning.

I have an 06 1200R and SEII slip-ons installed by the dealer. Flat labor rate for install only with NO DYNO! This dealer is a STEALER. Beware and be forewarned or you will pay dearly. If you don't want to do it yourself then find an independent shop in your area or another HD dealer. Don't be misled by this dealer.

DO NOT - repeat - DO NOT do business with that dealer. Period. If they're raping you that much over that then there's no telling what else they'll do.

You can do the pipes and air cleaner yourself.I did it without a manual and I am nowhere near mechanically inclined.A local jobber done my jets for 20 bucks.