I didn't and still don't have the stock tune and have no plans to change it, like I mentioned, the TOR's tune is still there for a reason should the PCIII, filters and secondaries be changed back. Mine works just fine, better than fine, Awesome.
Good that you are considering the triples and secondary removal prior to spending money to dyno, the D&D's w/triple K&N's canned PCIII tune is perfect for that. With the TOR's tune in the ECU, D&D/K&N canned tune in the PCIII, Triples, Secondaries removed in mine, it was so close to perfect that the dyno tune netted only 9hp and 8fpt in additional power. The primary benefit to the dyno tune in my case was to even out the delivery of fuel across the RPM range.
(I bet you go with a GiPro one day, how can anyone resist all the extra power you will have after all this in the low gears too?) lol