so you need ~7.4V, as much capacity as possible, in a 3D mag...
See, 18650s are longer than D cells by 5mm each, and they can only fit side by side in a mag body that has been double or quad bored. So that configuration would require 195mm length plus whatever length is added by whatever adapter construction is required to wire up the cells like that (3D cells is 180mm long), so the total length would probably be at least an inch longer than 3D size cell, which probably isn't going to fit in a 3D, maybe with some major tail-cap modifications and a very slimly designed adapter it wold be doable.
You could comfortable fit 4 18650s in 2S2P configuration in a 3D, and the wiring would be way easier as it would not require any odd center-plates to wire it up for 7.4V.
Another option is 6 17670s, these will fit 3 abreast in a tri-bored mag as I understand it. Wire the stacks channels in series, layers in parallel for a 7.4V pack with around 4.8AH capacity.
You could run 6 NIMH cells, I believe they make NIMH cells in 17670 size that are about 3.8AH capacity. They could just be wired in series in some custom pack, and then charged as a pack with a standard NIMH/NICD pack charger, no special balancing other than an occasional trickle charge required.
idduno if that helps any. If you do decide to go with a li-ion pack of sorts, I recommend a proper balance charger, and a pack built with balance taps to each set of cells that is in parallel. Or use a single cell charger, and charge each segment of the pack individually.