Flapper valve removed, pair system gone, shorter or longer stacks (stock or aftermarket), air filter changed - any one or all and more of those. It could mean anything.
I mean it's a stock bore, same cc, so crank stroke likely not changed. High comp pistons, flowed head, high lift cams, a few induction rubbers swapped and a re-map - nothing that would really generate 50HP increase and greater torque...
Any dyno outputs ?
Valve springy-ness is critical and often over looked if messing with cam profiles as it mostly falls within the "It'll be reet" range. And mostly that works ok.
Too weak, valves don't close quick enough, too strong and they'll float. Problem is RPM is variable so you normally only care about upper RPM, but resonances can occur lower down. Even with float they might not hit the piston, but you will lose compression and therefore power.
Summat like that.
For those mods - probably not far off as is. Not sure I'd bother, then again it'd annoy me not knowing.
Remap the ECU - IMHO never use a 'pre-made' map. Get one done for your engine.
Don't bother with a power commander, you really don't need it, and it'll probably give you problems in the future.
Sounds like something to do with 'Hill start' - did you accidently turn something on or off ?
So, more detail - cut out dead? , wouldn't rev but ran?, etc.
Exactly which lights were on on the dash and what were all the codes shown (it may be exactly as you said, but we've experienced many a time when key info wasn't given)