2012 CM2250 total demandate questions

[Auburn200x]

As the title states, I run a 2012 Kw with a ISX15 2250. It has be total de-mandated. No EGR, No VGT turbo, its all gone. Truck usually runs great, with an average mpg of 6.7. Never over heats. We did an inframe on it last summer.
10k miles after the rebuild, it started trying to make 40+ psi of boost, this was sudden. Today while driving it, it almost seems like it is having some turbo lag issues, then tries to boost sky high. This may sound odd, but the truck has always black smoked pretty good. When this change happened today the smoke cut way down and the mpg actually went up from 6.7 to 6.9 mpg. I've got it in the shop now going to test the CAC and all the boots, but I was reading that the wastegate could need adjusting. Also, not sure if it related, but it only has stage 1 and 2 jakes, no difference on breaking power with the switch in position 2 or 3. Any ideas on that?
We have insite and a good laptop, but I've not had a chance to try and pull the ECU program yet.