Yes! got it working, the solution (and apparently the ONLY solution), is a wooden pip on TOP of the Automated Crafting Station Mk2. Which I lead into cobblestone transport pipes to a chest after powering the wooden pipe with a redstone engine...odd configuration, but it works.
[uPDATE] It only flushed out the units it had in the output box, making me think it was working but its not producing new units still...so one problem fixed, on to the next! (believe my filters are getting clogged by other components. They get stuck in the "ON" position, and when I remove the pneumatic pipe, other components pop out...so I need to figure out how to keep stuff from going into the filter.