I performed a similar upgrade to my Mikado Jr. By installing a cruise commander (not modular). However, I had the same issues with my chuff sounds being intermittent, or seemingly locked in a stationary mode, with all other sounds working. After several teardowns and even swapping boards, I did not get anywhere. Then I realized it was the cherry switch. At first I changed it out feeling it must be intermittent since it was soaked in smoke fluid from my overzealous daughter servicing the smoke unit. But still, I had the same issues. Then I happened to test the loco without the boiler, and everything worked fine!
I soon realized when I placed the boiler shell back on, the wiring was forced down into the area around the cam and switch. My switch simply was being blocked, thus no chuffs, or intermittent chuffing.
I really think you should look at the cherry switch and test it, ensure it is free of obstructions, and lastly, ensure it is adjusted correctly.
Take it from someone who troubleshot it the hard way first. Despite being buried under the smoke unit or boards, the cherry switch was an easy fix. I just wish I had realized it much sooner.