MakerBot Print is our newest print-prepration software, which supports native CAD files and STL assemblies,
allows you to interact with all your printers via the Cloud, and many other exciting new features.
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.)