So I have been searching on forum for a while now and I have not found my exact issue so far. I did find this thread:
D90 ExMOD 2.5 NA SW Stalling out - Defender Source
Which I found useful, but not quite the same issue.
ISSUE: It seems the alternator will charge the battery slowly at idle, but once the engine revs increase charging pretty much stops.
So after the (very wet) Lost Coast trip with NCLR I developed a charging issue in which at idle around stoplights, stuck in traffic, etc the truck would stall. This would also happen occasionally while driving.
Once this started happening I got a multimeter hooked up and I was able to watch, once rolling to a stop during idle, the voltage starting to plummet. The only items on were the lights or the electric fan. Once these were turned off, the voltage would slowly rise.
Another member and I took some time and sorted out the engine bay and came to the conclusion that the alternator was good (tested several different ones all provided same result), and that the engine harness is solid and has good continuity.
Battery does not have a draw on it when the truck is off. I have also disconnected the electric fan circuit, but no change there either.
Recently on the drive home, I discovered that the fuel solenoid connection was loose and this has been repaired, however the issue remains, that the alternator does not seem to charge at full capacity.
I have on order an ignition switch, although i am not 100% confident this is the answer. Thought I would reach to you folks for ideas.