2007.5 LMM Tune Help!

Brand new stock ECM installed in truck. Truck has been deleted by previous owner, and came with EFILive AutoCal, with a DSP5 tune from Diesel Dudes. We ran the truck before the tune and it ran great, drove great, idled great. Only thing I saw was large puffs of smoke whenever I hit the gas hard or was going up hills. When we got back, we decided to go ahead and retune the truck with what the previous owner said he used for the tune. I bought another VIN lic from EFI Live, and then we tuned the truck, keep in mind that we have not installed DSP5 switch as of yet. The tune worked loaded just fine, did the count down thing and then removed the Autocal and started truck. After truck was started it idled fine all up until we decided to drive up the road and the truck shot me the reduced engine power message and it is like it would not shift past 2nd gear and would not go faster than like 15 mph all the way back to my house. Cut truck off and back on, it idles just fine but again still have engine reduced power and cant get out of that for some reason I do not know as I am new to all of this. Before the flash, truck was driving great but had a bunch of emissions codes. After flash, only had 2 emissions codes i.e fuel rail pressure ckt low etc etc and then a MIL malfunction DTC and that was it if that helps with anything..... Now stuck on what to do, need to get back running.

Thanks

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