If you use an SOB 1000 to drive an MC-E in 2S2P, it looks like the 2xLi-ions have to be able to deliver about 1.1A-1.2A of input current to the driver board. Thus, you might want to use 2xIMR16340 if you go with those small Li-ions. You are pushing the recommended 2C max discharge rate for standard Li-Co 16340s. Larger Li-ions like 17670 and 18650 should be fine without having to go to IMRs.
The SOB 1000 will generate about 6.6W of power to light up the MC-E in 2S2P, so you probably may want to pot the driver board to help dissipate the heat.
Also, besides 3xLi primaries, I think you could also drive the works with 4xLi primaries.
I don't see much reason to use a GD 1000 for an MC-E in 4P. Seems like it really limits your battery configuration choices vs using an SOB 1000. And for either board, the slightly increased lumens output doesn't seem to be worth the extra expense and effort vs a single die LED like a Seoul P4.