I kicked the design around for a few days. Not really getting anywhere with finding show-stopper problems. I can't simulated it, so probably best the spend $5 and get something to test for errors. Here's the schematic of what I released for fabrication:

I needed several ceramic capacitors on the CLP/CLN rail to prevent problems, since this is the power supply rail for the LTC4006 - added C14, and moved C12-C13 from DCIN to CLN. C6 is required to damp transients from causing an over-voltage condition on DCIN when an AC-adapter is inserted into the DCIN jack.

M6 was added to disable the buck and boost converters when the charger transitioned from constant current to constant voltage control -- effectively ending the charge cycle. 

I added a few CYA components. R17 is just in case the FB input of U4 requires a resistive input to remain stable. There is already a resistor at the FB input of U3. 

The finished PCB dimensions are 1"x1.2" -- pretty small. Here's the top layer:

It's amazing how small L2 is! There are Kelvin connections from the GND pin of the LTC4006 to its associated low current control components. All of the ground connections in the lower current balancing circuitry are made using vias to the ground plane on the bottom side.

Before ordering PCBs I opened the T16 case to make sure the charger would fit somewhere. I decided to mount the charger to the back case of the T16. The white patch in the middle of the case is a piece of paper that I cut to match the PCB dimensions. I'll probably just glue the charger at that location (the bottom of the battery case) then run the 12V power connections to a 5.5x2.5mm panel mount barrel jack on the lower left side, place the LED hole near the jack and run the thermistor through a hole in the battery case. The three wire connection to the battery terminals on the T16 will use a MR60 connector so that the back can be removed easily for future access. 

I got tired of looking at the PCB after 2 days...ordered 2oz. copper 2-layer PCB boards for <$6 from OSH Park. They will be ready in about three weeks. Hopefully the parts I ordered for it will arrive before then.