3v 3005-2010 mustang 4.75 stroker questions

the car has kooks mid legnths, jlt 110 (procharger going on after a few more miles) ford racing intake, deatchwerks 78lbs injectors dual 340 pumps and ford racing cams.
I did a mmr 4.75 kit, w displacement changing so little would it need to be scaled and if so what to scale? anyone have a base for a procharged 3v? also whats the best settings for these cams?
right now it stops pulling hard after 4500. it wasn't much better stock and do not know why. I bought it from a friend who blew it up and drove it many times in basic bolt on trim and it would not pull well after 4500 then, hell even when it was new it didn't lol maybe its a 3v thing?
last but not least after you cut the car off (to get fuel for example) then start the car if you get into it the wrench light comes on. if you let it idle for a min before you take off theres no issue. I have no idea why lmao
af is good I did move the vvt down from what ford rec by 1 degree and spark at high load by down 5 from 3k up for sake of the new engine having 10.5:! comp now but
that's all.
was thinking the wrench light may be from the displacement diff but not sure
thanks in advance! this is my first built 3v tune soon to be supercharged so any help is awesome!