I'm assuming you're not planning on fitting these pipes with bungs for a closed loop system. Therefore, your only choices for fuel mapping will be things like the VFC or Power Commander (but no Autotune). Given the one off nature of the pipes and the unknowns about the backpressure, it might be a good idea to have it dyno tuned once you add the fuel manager to make sure your fuel mixture is good.
As far as flanges, I would think any salvage 106 pipes would work. With as many people as have changed pipes I have to believe you could pick up some OEM's fairly cheap.
2012 Victory High Ball
Victory Stage 1 swept pipes and performance air filter
PCV and Autotune