It made me sick when you told me that the Shorai had failed on your trip. I have to say that of all the LiFePo batteries that are available on the market, the Shorai have had some issues, however I can say the same for others as well, unfortunately yours failed when it should not have. I have not experienced the Anti Gravity batteries yet, I believe that they are using A123 cells, but am not sure on that. I have just picked up a new cylindrical multi cell battery by Alien Motion (AM12) for my 950 EFI project, so far price and build quality are good. Time will tell if it will put up with the abuse of the 950. The Shorai in the 690 saved my bacon this summer where I was forced to repeatedly run the starting motor while troubleshooting a intermittent miss fire/stall while in the middle of no where trail. I believe that had the LA battery been in the bike still, I would have been attempting to push start the 690 on a very tight/technical trail... almost impossible.
Regarding the Braille batteries, you are correct that these batteries are OEMed by East Penn Batteries. I believe that East Penn produces quality batteries, however there are and have been failure problems with the battery when in the 950/990. IMO Braille is a very over priced marketing company, plain/simple.
It is technically possible to place a management module into the case of the Shorai for example, as there is extra volume within most of their cases to accommodate extra bits and pieces.
I have experienced either directly or indirectly about 5 failures of Shorai batteries, of these 5 batteries, 3 failed as a result of deep discharge. In all cases, Shorai worked with the customer to replace the batteries.
I believe that any LiFePo battery will have problems if the regulator gets wild with the voltage, which considering the VR on the 950/990, it can happen. The Shinden MOSFET VR is a excellent alternative that will ensure that the system vDC never exceeds recommended levels of a LiFePo battery.
Personally, I am hoping for a LiFePo starting battery with a BMS with protection and active balancing of internal cells. If I use batteryspace.com as a guide to cost, then a BMS with current limiting/protection, it will add about another $150 to the battery.... Additionally, of available tech from batteryspace.com as a guide, the BMS unit has a 100 AMP output limit. The starting motor in the 950/990 pulls about 300 amps peak. This is not to say that the technology could not be designed and applied to this application. Some time ago I probably could have designed and created this system, but my skills are very rusty in this area so I'm waiting for some other group to make it happen