which is a better choice for the 1/4. i know the 1-3 are steeper on a m12 but is the 3rd to 4th drop off too much. the setup is heads, cam, and spray with 3:90 gears.

 

M6 with those gears.

 

Tough call.

The m12 will definitely 60' better and that needs to be weighed against how much you'll lose on the 3-4 just like you mentioned.
NA would be a toss up but if you spray I'd bet you will run faster with the m6.
With the m12/3.90/spray the car will rev up so fast(esp 1-2) you will lose consistency and have more difficulty timing shifts,etc.
I would pick m6 and I've run both with many setups.