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To turn off the speaker, I just added a switch to the positive wire between the Amp and the PowerBoost.

For the headphone jack, I just wired up a very very short 3.5mm headphone extension cable, and plugged it directly into the pi. The volume is then controlled through the software.

Just drill a hole for the switch and jack, then glue them in place (I would have edited the files and modeled them in, but it was an afterthought.)