Do a search on exhaust or pipes or Supertrapp and you'll find a lot of information. You can also go to www.v-twinforum.com
and search on v-rod exhaust and get information dating back over a year.
To sum up your question the SuperTrapp is one of the better power pipes but it reduces lean angle so you'll probably grind it a little. The best power combo is:
No end cap and all disks (number of disks without end cap is irrelevant)
SE Air Filter (K&N)
Topless (remove air box cover)
EFI tuner of your choice HOWEVER, I recommend the HD Race Tuner along with a few hours on a dyno getting the bike dialed in.
You can go with the Power Commander PCIIIr and a downloaded map but it will only get you close and you'll still spend time on a Dyno anyway getting it right. Talk to your dealer and/or tuner and see which product they like. It's important that they are comfortable with the product you will be asking them to use.
Read the articles in the EFI and Performance section of this site, there's a lot of information to digest but you have plenty of time