HELP! Engine cuts out when shifting

Hey all, really stumped by this one so I'm hoping someone on here can help out. I've got a 2011 access cab TRD Offroad 6MT that has been acting up over the last week or so and I'm out of ideas.

Last weekend I replaced my master cylinder because the clutch pedal would get stuck on the floor. It was a bit of a pain and I ended up flushing the system quite a bit to get good clean fluid coming out of the bleed valve. The day after I replaced the cylinder, it drove just fine. The second day, I first lost power and the check engine light and the slip control light came on. I took it to a local mechanic that said it was a crank sensor error but I don't recall exactly what error code it was. He reset it (stupidly on my part) and I went about my day. A couple of times later that day while driving, I would lose power (engine would cut out, check engine light and battery light would come on but not the slip control) and I'd have to come to a stop and restart the engine. After restarting the engine the check engine light and battery light would go off. This kept happening and I couldn't explain why so I took it to a local dealership hoping they might be able to diagnose. One of the technicians after spending a lot of time with it said he was able to recreate the problem and said it was due to the aftermarket lighting I put in myself. I installed a Blue Sea fuse box in the engine bay and wired up some switches in the cab. I used an add-a-fuse and took power for the switch backlight from the passenger rear window fuse (access cab, so I thought this slot was unused) and routed wires and switch panel behind the shifter. The tech disassembled it and said that there was a connector that was in there that could have been shorting out and causing issues with the fuel pump and/or engine controller but that doesn't seem to make sense to me. Regardless, I took the fuse box out, removed the switch panel and replaced the add-a-fuse with the original fuse.

Now with all of the extra lighting disconnected, the engine is still cutting out and I can't explain why. I've driven it around the neighborhood a bunch and it cuts out sometimes when shifting from 2nd to 3rd, sometimes when I put the clutch in as I'm coming to a stop to downshift. Is it possible that it's the adjustment on the clutch? I didn't adjust the new master cylinder when I replaced it but it seemed to work fine the first day after I replaced it.

Totally out of ideas right now so any help is greatly appreciated. I'm also a little worried that I'm doing harm to the engine/drivetrain when it dies like it has been. Is that a concern? I don't really know how to diagnose it other than to drive it but if I'm putting the vehicle at risk I will just take it back to the dealership.

 

And now, twice in a row when I've started the truck up, the check engine light and slip control light comes on. My scangage is saying it's a P0335 error code.

 

P0335 - Crankshaft Position Sensor "A" Circuit

DESCRIPTION
The Crankshaft Position (CKP) sensor system consists of a CKP sensor plate and a pickup coil. The sensor plate has 34 teeth and is installed on the crankshaft. The pickup coil is made of an iron core and a magnet. The sensor plate rotates and, as each tooth passes through the pickup coil, a pulse signal is created. The pickup coil generates 34 signals per engine revolution. Based on these signals, the ECM calculates the crankshaft position and engine RPM. Using these calculations, the fuel injection time and ignition timing are controlled.

DTC Detection Conditions
•No CKP sensor signal to ECM while cranking (1 trip detection logic)
•No CKP sensor signal to ECM at engine speed of 600 rpm or more (1 trip detection logic)

Trouble Areas
•Open or short in CKP sensor circuit
•CKP sensor
•Sensor plate (CKP sensor plate)
•ECM

Sensor Location:

 

Yeah, that was the same sensor code that they were getting before. Turns out the first dealership I took it to incorrectly diagnosed it and thought it had to do with the offroad lights I added but it really does seem to be a faulty crankshaft position sensor, though I won't know until I pick the truck up after the service. The truck only has 99,000 miles on it and it hasn't been driven hard or offroad that much, mostly just fire and forest roads on camping trips. I have no idea how long those sensors are supposed to last but given their position on the engine, it seems like they shouldn't be malfunctioning this soon. Anyone have a similar problem?

 

Speculation is useless until someone trouble shoots that crank sensor circuit. I'd look at the waveform with a scope and try to recreate the problem. Or throw a crank sensor at it

 

Man, OP that sucks about that dealership. Too often lazy techs (not sure that term is deserved here) blame issues on modifications that have nothing to do with it. Hope you didn’t pay them!!
It’s an 11 year old truck at this point and sensors can and do fail. Either do as bro said, or gamble on just buying a new CPS and replace it yourself

 

Thanks for the input. I went ahead and replaced the sensor but that unfortunately did not fix the problem. The dealership I was working with was essentially of no help and they couldn't recreate the stalling when they drove it. They eventually suggested plugging a data logger into the OBD-II port and I recorded 5 events where the engine would cut out. I'm not exactly sure what channels they were looking at but they were able to confirm that there were stalling events that did happen but they weren't able to trace it to a specific component. I went back and forth with them for weeks and eventually just took my truck back. I purchased a VeePeak BLE+ OBD-II unit but I'm now curious what channels I should be looking at to try and diagnose the problem. I'm currently using the OBD Fusion app and it seems like there are a lot of potential channels I could be monitoring so any suggestions about channels to monitor would be greatly appreciated.

 

Go thru and check all your grounds. A loose ground could cause issues. Also check that all your relays, especially the fuel pump relay are nice and snug. I had a 94 that would randomly stall and it was a loose fuel pump relay.