Remapping the ECM i.e. Stage II will not gain you anything because you can control both timing and fuel with the PCIII-USB. The output you have is low for the configuration. For example, I pull the same amount of torque with 37g cams, stock heads, flat tops, 95" using Rinehart's.
I the dealer believes he can pull more power out of it with a Stage II, have him guarantee it in writing...sort of a bet. He's right, you pay gladly. He's wrong, you have a free Stage II and some Dyno time.
I am a bit confused on whether you had it on the Dyno or not?
In order to verify if he is an authorized
Dynojet tuning center go to this link
http://www.powercommander.com/centerbystate.shtml
Select your state and scroll down to see if he is listed. If he is listed, he has a Dynojet model 250 with the load control and at least one person has been trained at either Dynojet or an MMI school. That is the person that should do your tuning.
Easy way to tell if the have the right dyno is to get a look at it. If it is a 150-200 model like we have it will look like 200i on this link. Further down is a 250i with the load control unit on the left rear. The load control and the exhaust analyzer probes are what allows the tuner to
actually tune the EFI or even carbed bikes. Older dyno's like our 100 (updated to 150) limit the tuning to the same methods we used since they first came out. You read the chart and interpret where you "think" you can gain power or smooth out a section. Not a ton better than "plug chops" but, you get real world numbers rather than seat of the pants guesses.
http://www.dynojet.com/motorcycle_dyno/index.php