A few 2-Step questions

Let me share my setup and the issue I am experiencing before asking the questions....

MSD 7AL3 with built in 2-Step (Launch RPM) wired to the brake light switch and adjusted with MSD RPM Pills (anywhere between 2000-4000 is the range I have been using).

The 2-Step works great for launch RPM control every time. The issue is at the end of the pass, I am on the brakes to slow the car down and that activates the 2-Step causing havoc with the tach bouncing up and down and the occasional backfire out the exhaust. I assume this is due to the engine braking going on that holds the RPM above the set RPM of the 2-Step and the 2-Step activating since the brake light switch is sending a signal to the box.

My 727 has a RMVB without clean neutral so I have no choice but to engine brake so I am thinking of adding a separate switch (toggle) that I can use at the end of a pass to kill the signal to the 2-Step and allow me to use the brakes.

My question is, am I on the right track with this? How do you have your 2-step setup? Am I overthinking it and shouldn't worry about it?

Thanks in advance, Bill
Make sure you choose wisely, because you'll have to help me with mine lol