When I had my Softail I did the same. I had intake, Rinehart Crossbacks, and supertuner. pre 1000 they just put a fattened adjustment in. Once you have done 1000 miles you take it to them and then they fine tune everything with the Dyno. Same thing happened when I upgraded the 96 to the 103 and cams. at engine install they put a fattened tune in and after the 1000 miles they had me bring it back to do the fine tune adjustment..and Yes I did notice a huge difference in all the various stages... of new hardware vs new hardware with the fine tune..it was night and day difference.

 

I recently had my dealer do stage 1.5 on my Tri-Glide: A/C, Vance and Hines Headers and SlipOns, and SE255 Cams. The dealer does not have a dyno for trikes so they did "street tuning" using the SE PRo Super Tuner. I did not observe it being done, by my understanding is that they hook up the SE-PST to the bike and do multiple runs on a closed street (which they nearly have)...and make the adjustements iteratively. In the process they put 20 miles on the speedo and charged me for 3 hours labor.

I am very happy with the end result, the modifications accomplished what I was looking for...getting more low end torque to get my 1,500 pound ride up and going quite a bit quicker (including me and my co-rider), a better sound ,and eliminating the cat (a.k.a shin burner).