I did something very similar, except that I used the Soundtraxx 810078 medium oval speaker instead of the two smaller ones. It fit nicely between the rails of the tender frame, and I drilled a bunch of 1/8" holes (although not as tidily as you did! ). Rather than do a custom PC board, I just wired the decoder into an 8-pin plug and used the existing harness and just chucked the circuit board.
The only complaint I have is that I can't get the drivers to synch. That belt-drive means the motor draws so little that I have to have CV 116 cranked up to about 230, and it's still not perfect.
Did you try the sound before drilling the hole in the coal load? I don't think that at the frequencies those speakers are actually working at, and the size of that hole, you'd really see any appreciable difference. Besides, I'd think there's enough air leakage around the plugs to the loco that a small hole in the coal load wouldn't make that much difference.