The ThunderMax totally replaces your stock ECM, so the SERT modified map in the stock ECM isn't an issue. What you will need is a base map for the ThunderMax that is very close to what your bike needs. Check the ThunderMax site or call their tech support folks to see if they have a base map that matches your bike and any modifications that have been performed. I usually suggest that folks stick with a good dyno tune instead of relying on the so-called "auto tune" devices, but if you don't have access to a good tuner then one of the "auto tune" devices beats the heck out of the stock setup. BTW, you don't need a dealer to tune the bike with a SERT. Before you abandon the stock ECM and SERT you might want to do a little checking in your local area for an independent tuner.
Jerry
Jerry...thanks for your thoughtful response. I have the earlier SERT on my '04 Road King; it came complete with cables and software...it was built to 95" with the SE Heads, pistons, 211 cams, etc... and runs as smooth as silk...I have never had a desire to fix what ain't broke.
For this SE4 however, when the previous owner sent all the 'extras', only the module itself arrived. I haven't followed the SERT evolution over the last few years...does this mean I have to buy the software and cables separately? The previous owner is a great guy, but even more clueless than I am...he just turned the bike over to the dealer, had them install V & H Classic duals and a SERT tune. I suspect he sent what he has and the dealer just used their own software and cables(?).
The bike seems to run fine, with some occasional, mild deceleration popping and throttle hesitation when I downshift and apply mild throttle to maintain speed. It doesn't seem to run any cooler than my wife's with a Ness Big Sucker, V&H true duals, stock cans and the V&H fuel pak set to the parameters for that configuration. Hers runs well and gets better gas mileage. All of that seems to indicate that perhaps my SE4 needs some additional tuning(?)
You brought up a good point on seeking another tuner in the area. We are rural...as in really rural...however, there is a tuner in Pendleton, Oregon (30 miles) that is supposed to be good. He has the only dyno within a 120 miles of here..I can contact him and see if he has any experience with the SERT.
Thanks for you great advice.. Steve.