Not buying the difference, they did change in the older version from a 2 bolt baffle lock in to a 3 bolt on the endcap, and they did change the rear pipe bend due to cracking and mounted it differently along the way, but the shape and form are pretty consistent except that tehy went from having a 2 1/2 baffle to a 2 1/4. The 2 1/2 was the original baffle delivered, but after seeing a lot of early TC 88 not making power with the larger baffle they changed to delivering the pipes with the 2 1/4 and finally did away with the 2 1/2. Later they added in the quiet baffle at 2.0 and the peformance baffle at 2 1/4.
Have you run the bike on another dyno to be sure it is not dyno specific? What product are you using to tune the bike? Did they do any of the adjustments on the fly by wire that are now available in the Super Sert or the Mastertune? Have you compared the map the tuner made for you to the factory map he started with? Especially the timing tables?
While I own and have owned several D&D, i would rather stay with the rineharts as I prefer the sound / tone more. FWIW: My 07 SEUC 110 had the rinehart true duals with the 2 1/4 baffles in it and it made 127 / 122. I have the D&D on the 05 SEEG and it is coming off next day or two. My roadking has the old rineharts with the 2 1/2's and has no problem making power. Michelle's 04 SEEG has 07 Rinehart True Duals with a 103 and is making 117/115. While the 2 into 1 will bring your torque up on the low end it and the D&D is one of the better 2 into 1's I think you are barking up the wrong tree for your answer on the lower than expected numbers.
Are you absolutely sure your not sumping?