Alright folks, I'm back for more help. Recently got some bad fuel from a Giant store--Western Refining delivered bad fuel in the 4 corners area and a Durango Giant was supposedly the only station in CO to be delivered the fuel. I, during one my three fill ups this year, happened to be at this station. Truck died in work parking lot when I got off at 3 am. Not knowing about this fuel f up by Western, I changed fuel filter, bled VP 44 at the release valve (I have no idea what its called) and the banjo bolt. Got nothing. Learned about bad fuel from a trucker who is a bar patron. Added fuel stabilizer (PS supplement + cetane booster), to the tank and a few drops into the fuel filter reservoir. Rebled and primed. Attempted to jump start as I had killed the batteries prior. Truck turned over and died. Got help from another buddy and hooked a cummins to each of my batteries, got truck to start and has been running alright for the past few days.
This has brought about some new issues though. Both my batteries were shot so I replaced them today, and my alternator test at two different stores comes up reading NA the the diodes/lamp and passed for regulator and rectifier. I have been reading on moparman's site (Torque Converter Lock / Unlock Issues) that bad diodes will cause torque converter lock and unlock issues, which I do seem to have. When driving exactly 35 mph my truck is constantly changing rpm by about 200-300, and since the double jump start my headlights dim suddenly after a few minutes of driving .
Should I replace the alternator? If this diode thing is a reoccurring problem, should I replace it with a more powerful after market one?
This fuel problem may have messed up my vp44, or maybe my lift pump as the truck does seem a little groggy, or I'm paranoid. Would a new alternator help the VP44? in other words, before going through the fuel system and checking for pressure, should I get a new alternator?

Once again excuse my ignorance, and thanks in advance!
Ethan in Durango

 

Replaced batteries and alternator with a direct stock replacement. The headlight dimming was fixed, and the surging has also much improved.