Inside of that space, you could actually fit 9 18650 cells if you wanted, 3S3P for ~11.1V ~6.6AH depending on the cells...
pack size would be roughly 7cm x 4cm x 9cm after shrink-wrap and wire taps and stuff.
Provided you get a balancing charger that can handle the number of cells that need to be balanced you can charge the whole pack up at once, for an 11.1V pack, you will need 3 balance taps, the cells that are in parallel don't need their own individual balance taps, parallel li-ion balances itself out. Just treat each pair of cells in parallel as a single cell in the wiring...
Another thought, if you can come up with ~7cm x 4cm x 11cm you can fit 12 18650 cells, which could be wired as either a 3S4P 11.1V 8.8AH pack, or a 4S3P 14.8V 6.6AH pack. If the application can handle the peak voltage of 4S3P configuration (~16.8V) then that configuration might be preferable, as running higher input voltages can reduce current requirements, which allows cells to deliver closer to their rated capacity, also.. which increases efficiency of the whole system by reducing the effects of resistance.
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just thinking out loud here about some NIMH solutions that would offer slightly simpler charging methods..
10 18650 (A size) NIMH cells would be a nominal 12V with ~4AH depending on cells chosen and would fit in ~7x4x9cm space.
12 Sub-C NIMH cells would be 14.4V as high as 4.5AH depending on cells. and would be a really tight fit at ~7cm x 4.6cm x ~9cm
I think you could fit 30AA cells in that space... In fact, it would be very tight, after shrink wrapping and wiring, it might be too big. Envision cells laid 3x5 configuration, then 2 of those on top of one another, that should be exactly 42mm x 70m x 100mm before shrink-wrapping, a neat tabbed soldering job might keep everything small enough. The pack would need to be wired 10S3P, and would have ~12V 6-7.5AH depending on the cells chosen... The problem with this big of a NIMH pack, is that it's going to be hard to keep all the cells healthy. I think it would require separate charging taps for each section of series wired cells...
ok.... I've had my fun brainstorming..
Eric