I'm probably going to cut the cowl for the stack and include it at first.

It seems weird that removing the cowl makes that much difference, since the stack itself protrudes from the cowling. I know a couple of guys that just finished maidening new planes with gassers - maidened them with the cowls off, and after a few flights, they put the cowls on - each time they had to retune the carb. I believe tha they had to richen them. Maybe the cowl was trapping air at a higher pressure and forcing more into the carbs - 2 engines were brison 2.4's and one was a Hot-rodded G62.

You think that the air coming in the opening in the front of the cowl is pushing through the opening for the veolcity stack and causing a lot of turbulence? Where's a wind tunnel when you need one.