your build can be alot more compact. instead of using the redstone approach to create cobble, use the igneous extruder from thermal expansion.
it only requires 1 bucket of water and lava to infinitely create cobble. place the extruder ontop of the recycler and you don't even need any tubes or pipes
you'll need to put in 1 or 2 overclock upgrades in the recycler for it to keep up with the extruder.
then you could put a wooden pipe on the side of the recycler with an autharctic gate, set to energy pulse when items in inventory.
then below the wooden pipe you put the packager, that way you only need 1 wooden pipe, and no timers or anything.
then on the side of the packager you can place a filter, since a filter automatically ejects from a packager without needing any redstone ticks.
you can then place the deployer right next to the filter and about 1 or 2 blocks away the transposer, the deployer for deploying the scrapboxes, and the transposer to suck up the items.
you can then use another gate with a gravel pipe next to the deployer set to an energy single when items in inventory, that way you again have 1 less timer.
to make it really fancy you could run a red alloy wire from the deployer gate, that goes into a repeater set to a longer delay, that goes to the transposer, saving you another timer.
sadly there's 1 flaw in this design, if the deployer has more scrapboxes in it's inventory, the redstone signal will stay on, thus not providing anymore redstone ticks, though normally this shouldn't happen if you keep the chunk loaded and if the creation of scrapboxes would not be so fast.
