Hi, so theres a bit of a story and i will do my best to explain it.
A pulled a 90 K100 16V out of a barn after it had been sitting for about 10 years, it only had 20kms on it.
I got it going and rode it for a short time, during that time i removed the faulty ABS.
It became apparent that during storage everything had perished and i pulled it apart to complete a rebuild.

I put it back together as a Cafe Racer, put a BEP 3.0 in to replace the dash (tried before i pulled it apart and worked fine).

After putting it back together i couldn't get it to spark, initially i went over all my earths and connections, they've ll been clean and lubricated, twice .....

I replace the hall sensor with a new out of the box replacement, still nothing.
I checked my coils and i have a green constant when you turn the key and a black and red to one coil and a black and blue to the other, i checked both earths on the coils as well.

I replaced the HALL sensor thinking that it was the most likely cause, the Fuel injection and fuel pump are working(and was before this) but thought it may be effecting the spark.
After this i replaced the computer and also the Bosch ignition module.None of these things have made any difference.

What i have is a black and white wire coming into the Bosch ignition module.When you turn the key its earth, when you crank it over it turns to a power going into the ignition module.
Then at the coils both the black/red and black/blue have power to them as well as the green, but no spark, funnily enough the tester made the black/blue wire earth and the spark plug sparked briefly so the coils and the leads are fine.

So, what i'm wondering is should the black/white wire pulse and if so is this from the HALL sensor ?
Any help would be appreciated although i understand that 

Any help would be appreciated as i'm stumped, i got a mechanic to come and have a look and after about an hour or two he was stumped as well.  The only wiring altered was adding the BEP, i have tried it with the factory dash and its made no difference.
I've replaced the Hall Sensor, Computer, Bosch ignition module, all new apart from the computer.
I hope this makes sense,
Cheers
Mike

I don't have the exact detail on it but the Ks need a neutral light to start. Or the clutch switch. I suspect your issue is the modification necessary to overcome this. Swapping the original cluster requires a modification and there are threads on the forum on it.

The gear position indicator switch feeds to the original instrument cluster and also provides the neutral light. On your original cluster and wiring that neutral light was necessary to get the bike to start.

There is also a clutch switch which if you have no neutral light will allow a start.

I am also not sure if there is a side stand cut out switch on the 16v K100, if there is you won't start with the side stand down even if you have a neutral light on or have the clutch in.

Going backwards all was good until you removed the instrument cluster and fitted the BEP unit. This suggests the original parts were all in good order and you should look at the neutral light. As an aside you also need to make sure you have a charge light so that the alternator will kick in.

Someone will come in with all the technical info but that's my take on it. Don't bin any of the parts you took out as they are all likely to be good.

The black-blue wire is the feed for the rev counter.

Thanks for the quick replies ! 
I have tried the sidestand and clutch switches, they will kill the pump if they are not made and the pump is working, as they are a 2 wire switch - 1 in 1 out i think that as they will allow the pump to work they won't be effecting the spark.

The neutral switch did not occur to me so ill have a look at that today, I can plug the original dash back in as the BEP is plug and play, it worked fine before with the BEP and it still doesn't get spark with the original dash if i plug it in.

The black/ blue wire goes to the coils and also the rpm,i havn't changed any wiring apart from adding BEP so everything should be back where it came from, obviously something isn't though .....

Yes i am getting a growing collection of spares in saying that, the new ones will never wear out if i can't get it started

In case you don't have it, below are schematics for the engine and frame electrics on the K1004V:
https://drive.google.com/open?id=1_qBDOpFSr2UYykvCABkcXBm7wcIKGrLq
https://drive.google.com/open?id=1CpDM_uQ_92imAceOjVMgx7USI4ukdARO

The BEP3.0 should emulate start enable if the gear box is in neutral, if you have wired it up properly. Maybe check your BEP wiring.  In any case, pulling in on the clutch will enable starting as well.  asside, the BEP 3.0 does not interact with the ignition or FI circuitry, so it's presence or absence should not inhibit the bike starting only in so far as it generates a start enable signal from the TGPI switch. As an outside the box thinking, I might try disconnecting the Black/Blue wire from the BEP3.0 if possible. The BEP might be dragging that line down, causing ignition problems on coil set 1&4.

Yes, the sidestand switch needs to be working for the bike to start.  Since you say the pump primes when you turn on the ignition, then the sidestand switch may be in order, but best to double check anyways with a meter.

The Black/White and Black wires are input signals to the ignition amplifier from the Motronic, telling the ignition amp when to fire which coil set.  Neither the Black/White nor the Black wires are from the hall sensor. The HES feeds the Motronic and the black/white wire comes from the ignition amplifier.  The two components (HES and ignition amp) interact with one another through the Motronic, but are not directly connected to one another.

I searched for information about the pinout on the Motronic 2.1 ECU but failed to find much useful information about the signals.  I was able to find out that the pin to which the Black/White wire is connected is known as Z2 and Black is known as Z1.  I also found this guide:  

http:\\nearlyfreesoftware.com\pics\k1100_motronic_2.1_by_Frank_Warner-1.pdf

It doesn't specifically address your problem, but it does include a hand drawn diagram of the pinout on the Motronic 2.1 connector.

If you're going to debug the ignition circuitry, it would be helpful to get ahold of an oscilloscope so that you can see the pulsing that occurs on those lines.  For example, the waveform you should see on either the Black/Blue or Black/Red wires on the primary side of the coils should resemble this:



As you see, even on the primary side of the coils, you're dealing with 80 volts or more.  Be careful.