The Thunder max will not fix your problem....I'm not saying the tune up you have is good or bad however the Freedom mufflers you are running with 2.5 to 3'' baffle will never run good between 2000 and 3000 rpm. The baffle is going to kill the low end tq no mater what tuner you use. Then link a top end cam to the equation in the 257 cam and the dip at low end will even get worse. The next time you have it on the dyno try covering up 50% of the muffler at the end with a 2x4, on both sides, run the bike again and you will see the dip subside and tq get much better than it was before between 2000 and 3000 rpm.
Don't waste your money on more tuning or a Thundermax.....it won't help. The S&S header is fine, the 257 cam aren't bad, however the 2.5 to 3'' baffle will kill your low end.
Once you get a good muffler then get a GOOD TUNE, your mileage and power and smoothness will get much better....!
Doc