2014 CAT CT660 Shutdown

I have a CAT CT660 with a CT15 engine. driving downthe road the truck shut off. tried to get it going to no avail. towedto my shop and two out of the three batteries were flat dead. replaced all three, cleaned all of the connections, truck would turn over slow but not start. put charger to new batteries and after 2 hours of cranking, it slowly picked up enough crank speed to fire. Missing on number three cylinder. swapped injectors, didnt change. new injector harness installed per CAT. didnt help....... any ideas

 

Took all the grounds off starter and frame. Cleaned with scotch Brite pad and reinstalled unplugged ecm and checked for bad pins everything looked fine there. It turns over the same now. Fires up within 2 flips but still misses and smokes. What would cause the batteries to go from good to junk going down the road. When I say junk a battery tester said one had 11 CCA and the other 16 CCA. The third battery was still at 875cca. I know connection's could cause it not to charge etc but it reads that it's charging at battery studs on a multimeter.

 

Further update. Had valve cover off today so figured I'd presureize cylinder 3 and see what happened. Upon turning crank to get all the valves to close..... The exhaust side never got loose. Tried backing off adjustment a bit to see if it was just close enough.... Nope backed off all the way it's still tight. Pulled jake brake and rocker shaft assembly. One exhaust valve came up 1/2" higher than the rest. (3.3" vs 2.8")