New truck, someones been playing with...

[dhirocz]

Hi all. Been looking at the forums here, lurking for awhile.
Recently made the plunge and came to the O/O side of things. Got a good deal on a 2010 KW T2000, ISX15-400, 13spd, new clutch, still in great shape, 600k miles. Clean ex-fleet truck. I was looking for an older truck, but pulled the trigger after educating myself here. Have had the truck for a month, and so far hasn't given me any issues. I pull road tanks and ISO tanks, some overweight loads, and some in the mountains.
I noticed while going over the truck and servicing it that the DIC tells me it's got a 2007 ISX. Truck is a 2010 and I notice the emissions sensors have been replaced. Also, the regeneration switch is missing with a plate over it (connector for the switch is in the dash) This indicates to me that the emissions have been fooled with. All sensors are still present. Haven't pulled the DPF but I'm assuming it was fooled with too.
I was planning on doing a number of things to the truck prior to this...cleaning out soot, overhead adjustment, oil sample, filter mags, bypass oil filter, full lube and wheel balancers, APU servicing, stainless coolant tubes and silicone hoses, new filters, new shocks, air leak check, blah blah...try to keep the truck up the the same standards I keep my cars at (which is pretty damn high). Some of the work I've already done. I believe aggressive PM minimizes the risk of breakdowns and believe in it completely. I intend to modify for reliability and mileage.
I am familiar with ECM tuning and fuel injection, on cars though. I've built engines for my toys, port my own heads and intakes, and have even considered mildly porting the truck parts when it comes time for an in frame (just to clean it up, not to open it up).
I have noticed a few things I find odd, which may be from me coming from a 06 C15...accelerator hardly does anything until I get to about 50%, slightly lower than expected fuel economy ( doesn't matter too much how it's driven), very fast engine deceleration (I have to float very quickly, twice as fast as with the cat), odd turbo behavior (audibly spools up and down irregularly at part throttle)
Firat instinct I had was to flash the ecm to the correct configuration, but I'm afraid doing that might cause alot of downtime in fixing other problems and I just started making money with this truck so I'm not exactly sure on how to proceed...
I'm good with everything working as factory intended, I'm just trying to not go bankrupt while fixing it up 100%. Kids still need to eat in the meantime.