My take on your question is that, 1) just tuning and dyno will not make a noticeable difference to a bone stock bike? 2) The exhaust is the big restriction and the header manifold is more important than the mufflers.
While I have yet to find a dyno in my area, I tried to quantify the changes I made to mine one step at a time. Briefly this is what I found and reading all the previous posts on this subject tend to verify these findings:
Just a new RamAir filter = No change at all (except a lot of noise from the bear claw)
Tors + RamAir = Not much again, but more noise from the tail pipe
Tors + RamAir + Hanso tune for the change = Now we're getting somewhere
Tors + RamAir + Hanso tune + open the secondaries = Another noticeable jump
Paul Bryant header + Tors +RamAir + Hanso tune with opened secondaries = Hang on! The header was the single biggest performance boost without question! Completely different bike and the most noticeable gain for me was right where you're talking about. Low end torque. She started pulling harder and smoother in that low to mid range RPM which is exactly what I was looking for, not top end.
I then added PCV + AT and it did absolutely nothing except drain my wallet of $500 dollars. I wasn't really expecting much here, but new I would need it for the eminent Dyno Tune which hasn't happened because there aren't any tuners on the east coast apparently
Along the way I also tried stock mufflers that were "gutted" of the CAT's inside. I didn't like the sound/noise of the TOR's so I went back to this pair of pipes and to my surprise she pulled even harder at that lower range and She's much quieter now for the long cruises!
If I ever find a reliable dyno tuner, I will take the 3 different sets of pipes and quantify the results but for now my combination is
Paul Bryant header + de-cat'd stock mufflers + RamAir + Hanso tune w/open secondaries + PCV + AT
BTW, I have a Corbin fairing with a taller shield too. While I don't have any torque/HP numbers to spit out I can tell you that if I snap the throttle in first gear the front tire will come off the ground and sometimes if I time it right in second with a wee bit of a hill maybe, she'll come off.
My opinion is that if you're looking for the maximum gain without going inside the engine, get the header first!

You'll forget you have a windshield.
