Hmm. A weak cell in eother lipo wouldnt explain the charging imbalance, it would just mean that cell self-discharges quicker once removed from the charger (come back to the lipo after a few days and one cell will read 0.2v lower than the other or there abouts).
What is odd that it only does it with one battery and not the other- have a look at the balance taps on that lipo and check it isnt loose, and that the metal contacts arent dirty either. I would be inclined to say its a charger fault rather than the lipo- if you're charging it in balance-charge mode like you said, and its set up correctly (5amps charge rate and 2s lipo), then the charger should stop pushing current to the cell thats climbing too high, and in actual fact drain it down slightly until its back at 4.2v, then add extra current to the lower voltage cell until its upto 4.2v per cell (long winded sorry).
That issue aside, you've chosen a nice tidy setup and list of upgrades. My only question would be are the novak pinions hardend steel, or just aluminium? If its the latter, keep a close eye on them as they will wear down very quickly against the steel spur gear.
Our industrious lord and master Mike sells pretty much the best pinions available that will work on the savy,
these or
these (mod 0.8 is essentially the same as 32pitch, so they are interchangeable as such).