on the 2006, SEUC you are a bit off. All of my stock bikes 253 cams, air cleaner and pipes have made 98 torque and 93/94 hp. I have had 4 of these bikes and that was with rinehart true duals.
Doc is correct in that something is a miss. I even took an axtel 107 build did nothing to the heads and made 119 torque / 107 hp with stock heads and a S&S 570 cam. The compression was way too low, but it still ran pretty good.
First thing I would do is call the tuner and find out what gear the pull was done in before you allow this to eat at you. Then I would look at the tune. If the lifters turn out to tbe the issue you might consider the S&S's, sorry I am not into the hype of the Woods over priced lifters, the 99b's from Harley used to work well, but I have no confidence in the 99c's they just came out with and will stick with the S&S lifters.
If you are unhappy after all the changes you might consider what a lot of my buddies are doing, it's a nice package done by John Sachs with the 103. Most are making 112-118 toque and 103-109 hp using the stock throttlebody. He utilizes your stock heads cleans em up and decks them a bit and adds in a cam and tune and your done. Now that I have said that, let the we can do that too trolling begin.