Minecraft Java Edition – How to Control Where Items Get Stored Using Feed The Beast and Applied Energistics

I think they're landing on the transposer at the bottom of the pit, not getting pulled in because it's full, and despawning.

Really, this needs the BC pipes removed to work better, and there's no reason to start with a RedPower2 transposer, switch to Buildcraft pipes, then go back to RP2 tubes. Just use RP2 tubes throughout. That won't prevent problems when the Ender chest fills up, but it will stop this side of the system from leaking items.

To prevent the Ender chest from filling up, you really need more item overflow storage. There should be enough chests that you keep empty at the end of your tube system that they can store about half the entire quarry output, if necessary. I would combine that with an overflow just before it for just cobblestone (using a filter) that would redirect cobble you can't store into a recycler or an obsidian pipe/void pipe assembly, since you don't want your emergency overflow to fill up with cobble and render it useless.

To keep the overflow useful, always make sure to empty it before starting a new quarry.

Routers are, in my experience, your best bet here, you can configure one router to pull the scrap out (set the router to extract from a side), and one router to insert the required items (insert into top).

This way you need one Export/Level emitter per type, up to a maximum of 4 per router (technically you can add more per router, but it's messy). If you want more than 4 types of items you can add another router set to insert at top without problems.

This setup would also be easier to expand as you would just need to run IC2 power further and add the block next to the existing system. (http://imgur.com/a/wdnDY)