Iselbulls,
There is a bit of difference in these 2 items.
1. Racetuner only uploads a code that is written into the EPROM of the ECM.
2. It allows you to set timing per cyclinder
3. It raises the RPM Limiter if desired
4. It works off volumetric efficiencies
5. It is capable of removing decell popping as well as having a " Fuel Pump " feature
6. No additional hardware on the bike.
PowerCommander
Powercommander allows the tuner to tune and have no clue what he is doing just by holding the throttle at the correct positioning, software can do the rest.
Powercommander lies to the ECM and either adds fuel or takes it away. It can also do timing but its for both cylinders at the same time.
You are able to pull maps and upload maps on this unit without having to shut the motor off and restart the motor.
If you do not have a download from harley already in your ECM and your powercommander sheets the bed You will probably not want to ride the bike home due to if tuned with A/C and pipes it will be way to lean. This download also raises your rev limiter to 6200.
The difference here is that the powercommander is less expensive to tune until you add a Harley Download into the picture then it ends up being more expensive. If the best guy you have around is power commander these are the choices you will have to make. Also note that the RaceTuner is generally not always but generally limited to support at a dealer. This process takes longer so most of the tuners choose not to deal with it as much.
On the web right now you can from Ebay buy a racetuner for around 300.00. A powercommander will cost you from 289 to 379. Racetuner at a dealer is 459.00 if you get 20 percent off its 369.00. The download is about around 120.00 plus whatever the stealer will charge to put it in the bike .. 5 minute job ... most charge an hour.
As for pipes 2 into 1 if you want torque, If you just gotta have True Duals then consider a 2 into 1 with a falsey pipe (ghost pipe) or look at the Rhineharts / Vance Hines. I personally had a lot of issues with the rhineharts rear cylinder pipe, but BLM777 on the site has posted an install process he says has had no failures. You might go that route and see. I liked the Rhineharts only issue i had was continual replacement of the rear elbow whether installed at dealer, service shop or myself. I never got to try BLM's install.
Hope this helps,
-harry