Could you provide a screenshot of the factorization and EU method?
At the bottom right, you see my cobble generator. The transfer node has quite a few world interaction and speed upgrades in it. It feeds into the top of the packagers. Note that the pipes atop the packagers are Rationing Pipes. I realized as I was writing this post that that was actually a bad idea- not only are they unnecessary (they will insert no more than one stack's worth of any given item type into an inventory, but the packager's input slot can only hold one stack anyway), they were causing some kind of bug where the packagers stopped working after creating a stack's worth of compressed cobblestone. Use normal transfer pipes instead. They work fine.
The blue carped covers are to break any loops in the connections of the pipes- they make the pipe line follow an S shape over the top of the packagers. Why blue carped? It's the only cover that showed up in NEI in my Resurrection client. I blame Greg. If you don't like covers, you can use a wrench or a stick to turn the pipes into one-way pipes, directed in the same sort of S shape.
The crafting table is underneath the middle packager, and the second transfer node is directly under it. This node also has some speed and world interaction upgrades, although it doesn't need nearly as many as the cobblegen. It really only needs one interaction upgrade, and doesn't need any speed upgrades at all to keep up with the packagers, unless there's a really long pipe attached to it.
However, it's still kinda slow, because the packagers are slow. If you're worried about speed, it's probably worthwhile to exclude Factorization (at least for the first few stages) and look to other mods.
XU alone can do it pretty well. I found that if you take the setup in the above screenshot (with rationing pipes this time), replace the packagers with chests, barrels, or any other inventory that accepts cobblestone (protip: you can place trapped chests right next to normal chests, so alternating them works well), and place a duplicate setup right under it (with the covers slightly rearranged so it accepts items from the middle instead of a corner) such that the transfer node in the top setup takes the place of the central rationing pipe in the second (place a rationing pipe in this node's GUI so that it won't try to completely fill the chest below it with compressed cobblestone before moving on to the others), you can get a few times the output of the XU-FZ setup in twice as much space with the right number of upgrades.
It seems that putting more than one world interaction upgrade in a transfer node on a crafting table doesn't do anything. However, speed upgrades do make it craft faster. If you put 64 speed upgrades in the first node, you need only six in the second to just barely outpace it- if you have a sufficient cobblestone supply. I managed that with two dozen transfer nodes in cobblegen mode (i.e. attached to a block with lava and water on either side) with a stack of both interaction AND speed upgrades. This rig produces a stack of double compressed cobblestone in about eight seconds, or about eight double compressed cobblestones per second. That's probably slow enough that the packager rig could comfortably keep up and produce a quadruple compressed cobblestone every second or so, which could easily be fed through a chain of four more packagers with hoppers in between, for a grand total of one octuple compressed cobblestone every 9^4 seconds = about two hours.
Wow, Tema doesn't make bedrockium cheap.