OK , you said K1200RS (1999) modified custom project... Troubleshooting AT A DISTANCE something than has been modified OR hacked into is not an easy task ;-)
Given these limitations, let me try:
(1) Of course it is easier to troubleshoot with fuel pump noise... However even if the pump OR tank is not connected, you can check for this 2 seconds priming sequence (after ignition is turned ON) using a simple DC Voltmeter. On right side, where the lower original tank was, there is a 2 pins BLACK Plastic connector (confirm 1 wire is Green/White (this is +) and the other is Brown (-). See 1st attached picture.
Install your Voltmeter ahead of igniton senquence, then watch display for 12 to 13 volts (Battery voltage) for 2 seconds just after you turn igntion ON. After this Voltage drops to Zero UNLESS engine is cranked over (or started).
(2) Another item to check: if the main harness OR the warnings on dash have not been messed with during the conversion, after ignition ON you should see the RED engine temp warning on dash (this stay on until engine is started). If this RED warning is not ON, then the starter OR EFI Computer are off-line. This means one OR multiple interlocks are active (either side-stand, Neutral, Kill-switch, Motronic EFI fuse....). See attached 2nd picture.
When any of the starter satefy interlocks are active, you may still be able to operate the Starter (with clutch lever pulled) but the EFI computer will NOT give spark signal - neither will it operate the injectors or fuel-pump.
(3) Assuming the main harness has not been too much damaged / modified , you will also find a 2 pins WHITE plastic connector near top of fuel tank (1 wire is Yellow/Violet and the other is Brown). This normally connects to fuel level sensor (float) but it is NOT critical for function of EFI Computer or the engine electronics. You can still run the engine without this plugged.
P.S.: CLYMER manual for k1200RS / K1200LT is available directly from AMAZON in most countries (CLYMER part number is M501 with various suffix depending on revision / updated version). It is more complete than the BMW factory service manual with a lot more photos and details.
The electrical diagrams of CLYMER are not perfect (about 95% OK) but certainly better than the BMW shop manual where there is none (the Germans think you do not need this in a Service manual - amazing !). However you can also buy a CD with a Windows based software from your BMW dealer to get all electrical diagrams from 1993-2008 models for about $US$ 50 This is BMW part number: 01797720399 and all diagrams are one same CD.
Thanks for your quick suggestions. I know, assisting from distance is very hard to do, and my poor English does no contribute to that. Nevertheless the details in your suggestions provide me with more details then I could wish for. I had to reach out to an international forum as the Netherlands is a small country, not many specialist here, let alone online on a forum like this. And my German is only good enough for ordering a beer so that wasn't an option either.
So, since the kids are finally at sleep I got myself some time to check your suggestions;
1 Fuel Pump.
I've connected my voltmeter to the power connecter as per described but during starting/cranking the engine got no voltage indication on the meter.
2 Instrument panel lights
The RED temp warning indication is NOT ON when ignition is switch on. Also Neutral indication on dash is NOT ON (gearbox is in neutrol for sure as the rearwheel spins)
What does come ON are the Battery, fuel level and oil pressure light.
So you're deffinitly right about the interlocks that are still present.
I've traced the 2 cables (Brown/pink and Green/Black) from the neutral light to the INSTRUMENT CLUSTER CONNECTOR 2, and from there both wires disappear in the cable loom. GR/BL goes to a connection with several GR/BL wires and the Br/Pink wire that goes to a 3 wire "intersection"from where 1 goes to a BLACK 5 wire/6Pin connector and the other one runs to a WHITE connector from where the collor changes in Brown/Black.
Side stand is not extracted but IN and kill switch is working as when not in center position engine wont crank so i assume it works.
3 tank level sensor
Good to know these wires have no interferance in getting the spark back to life.
So if I am correct the first step is to ensure the Neutral light is back in business again. You can already feel the question comming; is there suggestions;-)
Supposed the EFI is not online, how can I check or re-establish this. Maybe some pins I need to check if they have 12V on them?
Tomorrow I'll see if I can get my hands on a Clymer manual or BMW CD.