Instead of the flap in between the two chambers you could use blackflow valves. That's what I did on my build. This allowed me to use any of the motors at any time. The image below shows my box sitting on it's back before I installed it:

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In fact, if you want those valves I'll sell them to you. I just pulled that box out of service. Which leads me to my next bit of advice: I don't think wood boxes are the best choice for a material for these. The motors get very hot. I had mine enclosed similar to how yours are. I even vented them. Ultimately I had to pull the back panel off of the box to keep the motors from baking.

My box had a cool baffled muffler system in it too, and it did knock down quite a bit of noise, but they were still loud.

When these motors fail, and the absolutely will they often times will spark, in fact when they start up, like most brushed electric motors they spark.

After a couple of failures I decided that it's not safe to run these in a wood box. I ultimately decided to buy the Black Box Hurricane. It's made out of all metal and it's well built. It's also much quieter than what I built, and has an intake filter.

I'm not saying don't pursue this, but I'd be pretty weary of any flammable/wood material. The Black Box seems to be about the best thing you can get that isn't a commercial vacuum system.