Hopefully someone has some ideas.

TLDR at the start: intermittent delayed crank on 2014 T4R Trail (not keyless) with 75xxx miles, new battery, clean terminals, started a few days after a water crossing, and occasionally throws engine code P0335 (crankshaft position sensor), vehicle in Park or Neutral with foot on the brake. I tried the search function and can only find the following related discussion without a posted resolution: My 4Runner Won't Always Start

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Drives normal except when it throws the P0335 code, then CEL with Trac Off, and 'Green Vehicle on level ground' lights are on.

If the vehicle sits for a few hours, then it is generally repeatable (delayed crank). If it has been sitting for less than 30 minutes, it usually fires right up. Put the key in the ignition, turn to 'on'. Let everything come up for a few seconds. Turn key to 'start', displays go dark except for dash indicator lamp lights. After 1-2 seconds a slight hum turning noise, but not a starter crank, is heard. No clicking or other signs of life. Hold for 3-5 seconds in 'start', then release to 'on'. Repeat several times and it will eventually fire the starter and start up with no hesitation once the starter moves.

When it first threw the P0335 code, I took it to the dealer (it also had a P0340 pending code). Dealer cleared code and was unable to replicate the delayed start (intermittent). Vehicle sat over night and it fired up no problems the next morning at the dealership. After about two days the intermittent delayed start began again. No codes, pending or otherwise, were generated by the delayed starts including holding the key to 'start' for up to 10 seconds. After 1.5 weeks, and a weekend of sitting off for 80+ hours, delayed intermittent start continued. After multiple starts/stops throughout the day, the vehicle had a ~30-45 minute off period and then struggled to restart. Threw a new P0335 code.

About two days prior to the start of this, the vehicle did go through a fairly high water crossing (2~2.5 feet) for 30 seconds, did not stop in the water and vehicle was off for 15 minutes prior to crossing. No water came in the engine intake or entered the diffs/transfer case. Small amount of water in through aft doors. Engine bay was fairly dry after water crossing and there are no signs of corrosion or debris on any sensors/connectors that can be seen at a glance. I visually inspected the fuse box incase something came loose from the weekend dirt driving and found nothing.

Any ideas on what's confusing the computer(s)?

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EDIT 4-4-2019

My suspicion now lies in the ignition relay. I put a new starter relay in and it continued to act up. Got fed up and as a last resort did some percussive matinenance with the key in the ignition (jingle jangle the heck out of it in all rotation positions (up down, left right, in-out...) and that seems to have helped tremendously... even made a pretty picture of start attempts vs starts:


I've now ordered a new ignition switch. After looking at the repair manual , I believe the switch engages the ECM, but is not 100% of the time engaging the starter relay. I plan to pull it and swap a new one in as soon as it arrives in a few days.

Any additional advise or theories are welcome.

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Edit 6-1-19

So the above 'key jingling' and such turned out to not fix it. Problem continued, intermittent as ever, after swapping out ignition switches. After a few weeks, later April, for about a week it would fire up on the second attempt which was livable. I had a week vacation where I didn't need the vehicle, so dropped it off at the dealer for them to hopefully duplicate and troubleshoot. They were able to replicate it twice but unable to troubleshoot it. This was in late April/Early May. After I picked it up, it has 'cured' itself. I'm beginning to suspect the dealer installed KARR 'security' system was misfiring for some reason. I want to take remove it since it's the only 'aftermarket' item spliced into the vehicle starting system. It's on the inside of the vehicle hidden in the drivers kick panel by the inside fuse box. Still not 100% sure what caused the vehicle start system to go berserk, but seems to have cured itself for the last month.

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i would check for a loose ground first, if you have a volt meter check cranking voltage at the battery clamp (not directly on the terminal). lastly try checking cranking voltage at the starter terminal if you can get to it.

Will have this checked. I’m dubious of a ground fault, as it’s not impacted by percussive maintenance. On -> Start repeat several times and then it fires right up. Hopefully it’s as simple as an obvious ground / starter cable... starter is in a heck of a fun place!

Now I'm normally on the Corvette Forum as a Tech Contributor but since my 2016 4Runner is so reliable I never have any maintenance issues but a car is a car as far as diagnostics !!...what do you mean by "delayed crank"...if I had a customer who told me this I would say "you turn the key and no crank and then a few seconds later it starts to crank"...is that what you have or is it just a "cranking no start" ??...P0335 is CKP sensor issue and 0340 is CMP...if it is a "cranking no start" does the Tach appear to move when cranking indicating ignition pulse ??...if no movement you must check for spark and injector pulse...you will have NEITHER with a bad crank sensor...I'll have to look for my crank and cam sensors locations but maybe you had some water intrusion issues with both...a cranking no start is the result.

Now if you mean you turn the key to start and nothing happens for a few seconds try having someone give the starter a whack while holding the key to start...you may even have an ignition switch problem. I'd also check if you have power down to the "S" terminal at the starter solenoid when the key is held to start...unfortunately I'm still looking for a 2016 FSM (factory service manual) but I'm not holding my breath !!...if you think it might be a CRK or CMP sensor I can show you how to test the wiring...it's a simple 3 wire Hall Effect Sensor...power, signal, and ground.

Thank you for the input.

Turn key from “on” to “start” = nothing. Hold for several seconds. Rinse and repeat and it will eventually crank and fire right up (1 crank = engine start). Tach gage is normal when running. Tach registers zero during delay crank, as starter isn’t turning.

Intermittency remains, and I've removed the 'delay' by not trying for more than one second. No start = back to "on", wait for display to power up, back to "start" (one second or less), rinse and repeat until she fires up (sometimes first try, sometimes 4th try).

I just pulled the starter relay from the fuse box and the vehicle acts very similar (whirling noise under the hood, TRAC and Green Vehicle lights illuminate). Relay and box look clean.

I'm guessing the engine codes are a symptom here and that the crankshaft position is just a phantom/related nuisance fault to the intermittency of starting.

Any other thoughts on what might be causing this before I find a new relay (PN 28300-21020)?

Like I had mentioned if the car won't even crank check the B+ terminal of the starter with a 12 volt test light connected to ground while holding ignition switch in start...light should be illuminated...you might have a bad ignition switch or something downstream of it...unfortunately like I said I need the wiring schematics...a bad cam or crank sensor is a "cranking no start"...have you checked the battery ??...full charge is 12.66 volts...have the battery load tested first !!

New info / update in initial post.