**Edit:Got it fixed with Pete's help! See below, I grounded too much!
Boy I'm beating my head against the wall with this one. I'm doing a full swap of engine and wiring harness to a different chassis.
Monday night it was running and warmed up. I shut it down and tuesday morning started to wrap the wiring harness in protective stuff.
I went to check to see it still ran, crank - no run. I'm assuming I screwed something up and grounded something out?
I'm tearing my hair out.
1994 Miata Chassis
MS3ProPNP
VVT engine
I've checked and swapped every fuse in the stupid thing.
The fuel pump primes on key on.
The main relay clicks and I've tried swapping it.
I've tried swapping cam sensor
I've tried swapping crank sensor
I've checked for continuity between cam sensor and ECU
I've checked for continuity between crank sensor and ECU
Timing belt is still there
I've checked and added grounds everywhere.
Thoughts?
Can you connect to the computer with a laptop to see what the computer sees?
I don't know about the PNP computers, but sometimes the regular MS computers can go into an electronic funk if the sensor ground connects to chassis ground. I'd imagine that the PNP box gets engineered to work with whatever the OE computer does, but at the same time, a lot of OE computers also follow the "sensor ground is tied to the engine computer not chassis ground" strategy, so if you grounded a sensor ground to chassis, that may cause issues.
First things first, can you communicate with the computer. If you can, check for RPM signal while cranking, make sure the coolant and air temp sensors read appropriately, make sure the TPS reads correctly and isn't stuck over 70% which will be clear flood mode, etc. If you can't, find the harness ground that you'd inadvertently stuck in the loom 
Thanks for the ideas - Plugged in to the computer I've got no RPM either, I'm not seeing the plugs wet when I key on and hear the pump, should they be wet for the priming pump?
I feel crazy, it started and ran perfectly and now I'm clearly missing something.
Throttle position, air temp, water temp, 02 sensor all show up correctly on the PC when plugged in.
Can you go into test mode and verify that the injectors are clicking and the coils are firing?
In reply to Pete. (l33t FS) :
I'll try when everything dries off, I tested the pump by disconnecting the "return" line putting it in a fuel jug, but I'm tired and mixed up the return line and feed - you can guess what my garage floor now looks like.
I also had a moment of concern and added fuel in case the gauge was reading wrong. Fuel pump is working and we do have fuel can also now be confirmed ...
Not the most practical method of verifying that it's running the pump, but that can be marked off the list
Jeez. Ok, I found the test modes as suggested. Nothing was working except fuel pump.
I think it was exactly as you said, I think I chassis grounded the sensor grounding? A lesson learned, more grounds aren't always more better.
Lol, I tore out all of my work that I had previously done so now to put it all back together. I was trying to get this car done for an event this weekend. Building an entire car in about 7 days wasn't the best plan.
In reply to Pete. (l33t FS) :
PS, you're awesome, thanks for the help. I owe you a (insert beverage), big time!
In reply to accordionfolder :
If you can connect to the computer without error (the other sensors are reading), the fact you are not seeing engine speed is a big problem- it shouldn't fire fuel or spark if it has no idea the engine is spinning.
In reply to alfadriver :
You got it right, 
TunerStudio/Megasquirt has test modes that will pulse injectors, turn on the fuel pump, and fire the coils for a fixed amount of time regardless of engine position. (Like Pete said there would be).
It turned out to be, too many grounds. This car was LS swapped before and I had a ground strap hanging there and bolted it on without thinking. I didn't realize I could "over ground" it.
One more for the road. Hilarious, I almost had it completely back together and now it looks like this. I guess nothing to do but to do it
It's also possible that disconnecting the computer corrupted something, or being unplugged while near cosmic rays and nanobeavers corrupted something, and going into test mode uncorrupted it.
Sounds weird, but I had that happen to an older PNP unit in a Miata. It corrupted something and was double-firing the injectors and doing all sorts of other weird things. Looking at the 3D view of the VE table, the "ball" was nowhere near where the engine was actually running. Simply opening every tuning map somehow resorted it and the car drove great again.
I'll update my actual build thread later, but since you guys helped save my bacon I figured I'd share here too. Maybe we're going to make it? My buddy Mitch came over and we hammered on it today.
