Misfire but only with MAF active

[apex2112]

I have an issue with a 408ci I'm trying to dial in, if I switch over to MAF only the engine misfires.
If I tune only the VE I don't get any misfire?
I'm trying to get my lower rpm fine tuned with the o2's so the attached logs don't have the wide band connected.
The 2 tune files only have minor differences other than one is for tuning MAF and the other is for VE.
The MAF sensor is new, replaced about a week ago.
What would cause the MAF tune to misfire?
04 2500 408 maf tuning with o2.hpt
maf_02_5-20-2018.hpl
04 2500 408 ve tuning with 02_2.hpt
ve_02_rev2_5-20-2018.hpl

[apex2112]

Well I jumped the gun, getting misfire with both tunes.
Seems to happen mostly at idle.
The SES light comes on, but shortly after driving light goes out only to come back once stopped again.
Would it be advisable to adjust the misfire tables under engine diagnostics/misfire?

[dermotw]

-You need to say what mods it has, cam etc...?

[apex2112]

408ci has 90mm throttle body, aftermarket intake manifold(Chinese knockoff), 60lbs Deatschwerks injectors, not sure of the cam specs he said "its a mild cam with .600 lift" and compression ratio is 11.1
In A 2500 4x4 with 38" tires