Engine won’t start after engine swap

Hi all
ive just swapped a M15a into my 2006 Jimny 
ive just tried to start it and nothing happens 
there are a few clicks that I can hear but the starter motor isn’t spinning 
Any advice?
i was wondering if the immobiliser might be a problem 
ive tried both keys
thanks for any input 
Tom

Just tried one of the keys again
Locked and unlocked the car a couple of times
It now starts and runs for a few seconds and then cuts out
Could this be the immobiliser?
Engine sounds sweet which is a bonus!
Tom

Now back to clicks and no starter!!

I’ve cleaned up the starter motor connection and it fires up now but only runs for 2-3 secs before cutting out again

First, the immobilizer won't prevent the starter from engaging and cranking the motor, that's going to be purely an electrical issue, and second, it's extremely unlikely that the immobilizer will allow it to start and then shut it down after 2~3 seconds.

Look at the dash lights, the immobilizer warning light is most likely an orange padlock, newer models might have blue & red keys, an immobilizer fault will usually show up as the starter cranking the engine over without it firing and the warning light on the dash flashing.

It'll behave like a no fuel/no spark failure because that is exactly what it is, the immobilizer shuts down the EFI system.

Start by testing for no fuel - spray starting fluid into the intake whilst cranking the engine, if it starts & runs for as long as you're spraying the fluid you have a fuel delivery issue, you can also check for a spark at the plugs.

Good old fashioned petrol engine troubleshooting techniques.

I'm going to stick my neck out, you have a fuel system blockage causing the pressure to drop below what's required to lift the injector pintles off the seat, there is enough flow to build pressure into a "deadhead" situation, but as soon as the injectors open, the pressure drops too low to sustain injection and the engine dies.

If it starts & runs on starter fluid, get a fuel pressure tester and verify the pressure.

Thanks that’s really useful
I agree that immobiliser is unlikely as there was no problem prior to the swap
I was wondering about the crank position sensor on the new engine as a possible cause.
Would a failed sensor cause similar symptoms?

Morning - I had a similar issue after an engine swap (though it was just another M13A) - turned out all the jiggling of the wiring harness caused some of the older connectors that were corroded in place to straight up break off with the stress of moving about.

I had intermittent dropouts of RPM, and the immobilizer was quite unhappy at times, sometimes randomly kicking in while driving, especially over rough ground.

These connectors were under the fuse box, but I would go through and systemically check all your connections, just in case, the electricals can get a little worse for wear with time.

Image of connector (I cut the red and white one which IIRC was just a headlight, the other two were corroded off with an intermittent connection):

it is a fuelling issue.
I sprayed carb cleaner down the intake and it kept running fine.
I've used the Swift injectors rather than the original Jimmy ones...could that be the problem??

Tom

Stop trying to guess your way through this, systematic diagnosis is the way forward - get a gauge and confirm the fuel pressure is within spec.

Failing that, use a noid light and see if the injector drive signal is present beyond that first two or three seconds.

Sounds suspiciously like a a grounding fault. The fact the starter motor was being feeble. I would check the engine earth strap as the fuel pump might not be grounding properly either. 

Sure, check the grounding, but, since the fuel pump is in the tank and doesn't use the "engine earth strap", I'm fairly certain that's not the problem.