Alright so I've seen a few post on here about this issue already and still haven't found a solution.. Quick run down.. Few years back blew the chains in this lovely 5.4 triton 3v, yay no surprise.. So I've had motor replaced with a rebuilt, that has fixed the bore issue in the factory motor.. All sensors have been replaced and tested. Still getting P0345 and P0349. now like I said the CSPS ( Cam position Sensor ) have been replaced , VCT's have been replaced , New cams were installed and timed by the motor company , Crank shaft positioning sensor has been replaced as well. The battery has also been replaced do to the fact that when looking up the codes it says it could be an issue but for some reason the battery is still draining which is telling me there may be a short but I cannot physically find one and truthfully I don't know how to locate one without just looking at the wire on the harness.. Now the alternator has not been replaced but I have done the old test of disconnecting the Neutral while its running and it didn't die off I don't know if that is the way to test the diode inside the alternator or not.. Also the starter has not been replaced either which again could be one of the issues * faulty starter * but I'm not running into issues starting the truck.. I am having hesitation and rough idle ( seems to still be in limp mode ).. When the motor was replaced I did have the PCM flashed considering those 2 codes are permanent codes and from what i found online it needed to be done.. I try to do all the work on the truck myself besides the huge replacements like motor.. Sorry I know this post is a little all over the place but I'm pulling my hair out trying to fix this have been trying for over a year now.. If anyone has any insight or tips or solutions please feel free to discuss.. THANK YOU!! ( also pig tails have been replaced and soldered for the CSPS )

 

Have you watched this video?
and this one?

 

THANK YOU

After watching these two videos i ran the test.. alternator turned out ok weird thing was only 1 code came back after i tested this P0345. So moved from that and went on to testing the VCT.. Disconnected the VCT and P0349 and P0345 did not come back but it did throw a P0020 which was letting me know that the VCT circuit was open. Assuming that was due to the fact the sensor was disconnected.. So i replaced the VCT, in doing so i had to remove the valve cover -_- snapped a bolt so it became fun.. While cover was off i checked the teeth on the Cam phaser , all where straight so ruled that out and also checked timing it was in deed in time.. After putting everything together tested it out 2 key cycles 1200+ rpm no codes!! YAY!! turned truck off for about 10 minutes started her up and low and behold the dreaded like came back to life with just 1 code this time and again P0345.. No rough idle minor power loss.. I inspected wiring to both sensor VCT and Cam Sensor all looks good.. Now i have replaced all sensor, crank shaft , Cam Shaft , VCT.. tomorrow im going to climb under and check the Crank shaft wire to make sure its good but im pretty sure it is.. Now with the VCT i found out the rubber grommet had a pin hole in it.. which caused oil to come out and some how managed to make its way into the VCT pigtail and sensor.. I have not replaced that pig tail but i did replace Cam shaft pigtail.. While running a live data test with snap on meter my VCT's were staying at a flat 0 now it did not have the graph like the video had so i dont know if it would show the flicker in the numbers on the screen but i figured if it doesnt show it that means im not getting any signal to the VCT's maybe change the pigtail out? there is 3 parts left that i could replace to on this truck that it could be.. Starter , Alternator , or PCM.. Ive been working on this truck for years now and can not for the life of me figure this out.. Is there a way to test if it is the PCM? i dont want to continue to throw money in to this thing.. As far as testing the voltage truthfully i have no idea what im doing or what numbers to even look for.. Please anymore ideas would be very helpful..