If you already spent the money on the SE tuner, that's fine, just realize you're going to have best results putting the bike on a dyno... The SE tuner is only going to give you canned maps for Harley recipes. All changes you're talking about are not Harley/SE.
Get your package together, install all at the same time, take to a dyno tuner with your SE module and you'll be good to go. Buying a PowerVision is a good option if you had not already dropped the cash on the SE tuner. They do the same thing, just different interface. A Power Vision does not mean no need for a dyno, but buying from Fuel Moto, you get maps for their 2-1-2 and slip ons which represents a canned map closer to what you're buying. Even FM will tell you once you start digging deeper, cams, modified heads etc you're probably going to need to get dyno tuned.