The simplest way to use a NANJG in a lower voltage system is to remove the reverse protection diode and solder across where it use to live. This will give you about 0.6 to 0.7V of extra room before low voltage protection kicks in.
PPtk
Is that how big the voltage drop on the stock NANJG driver's diode is!? That might explain a problem I'm having at the moment - I modified a NANJG driver to use a Tiny25 and my own value resistors. I find on high mode (2.8A) my drop-in is halving its output almost straight away (signifying the cell voltage is below 3V) even on almost fresh IMR cells. I might replace the stock diode with the one my code was written for (200mV drop) and see if the problem persists. I did wonder if this was the issue but your post seems to prove it. I was trying not to have to take the driver out for the billionth time!
Yeah, most of the stock ones i've seen are the cheapest, crappiest, silicon diodes you can find. 0.6V or more..
I've run across maybe one in all my years of flashlighting that was a low-drop schottky..
Of course your code could also be screwed up :) (JK Mattaus)
I have never seen an SST90. I have done but not completed the light, an MTG-2 direct to copper. I hope the picture can be of some help.
All of mine have Schottky diodes in them… I checked a half dozen or so from different sources.
I should have time on the weekend to re-build a new driver with my own schottky and it's known Vdrop. I'll see if the problem persists then. And yes the code could be wrong, but it's not mine so no skin off my back haha.
- Matt
Well that didn't fix the issue so it must be the code. Then again I should try it on my own hardware as well, not just a modified NANJG driver. Seen as it was written for my own hardware that would be sensible I guess haha.
On a side note I recently rebuilt my PC, got rid of Windows and have switched exclusively to Linux. It seems I backed up EVERYTHING excepts my eagle libraries. Now I have to re-create all my emitter and 7135 footprints from scratch. 
That bad, but can't you extract them from the schematics you have made?
http://slopjong.de/2012/12/06/eagle-extract-a-symbol-from-a-project-to-a-library/
Oh that's a great idea! I have done that before but forgot I could do it. Thanks 
PilotPTK
I have been away for awhile
do you still have your 28 chip boards available?
and if so, can you populate them with 7135s as needed???
Might be here