if i send the computer from my L99 to hennessey to get tuned will that take out the AFM and if i add aftermarket parts like a new cam, heads, headers and a supercharger will they tune it to work with these mods

AFM/VVT is mechanical as well as programming.

If you tell them the mods you have, they should be able to tune them in.

ok thanks for the reply do u know where i can get any info on how to completely get rid of the AFM
i would just get the LS3 but having the M6 where i want a dive it is gunna be a nightmare at least i think

You need to do a cam and valvetrain swap and programming to get rid of the AFM.

You can disable it in the tune.
If you want to remove the hardware you have to swap lifters, cam etc.
But you can simply just disable it in software!

I would wait to mess with the ECU till you are ready to do the other mods. Knock it all out at once, -right