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Thanks for all the advice guys, armed... i'm heading back to the garage tuesday on day off to hopefully progress.

on mine the block connector to the ignition barrel was causing the Atlantic 500 panel dials etc,  to light up and the petrol pump primer to sound,then they all went out, so i cut it out admitedly to the cheap Chinese Barrel someone had fitted,joined and  soldered it to a gash Honda one in my box of bits.

Only last week it started rattling like a pig after a fair speed blast, eased it home on part throttle, took the underseat cover off and found the brains that slides onto a connector on the the side of Fuel injector, (the electronic bit of the fuel injection gubbins that meters the fuel via the ECU) was loose, pressed back onto the bayonet and got full revs whilst on the centre stand
next day not so bright and sunny  took her out on leaf strewn slippery roads,  but on the the main drag the ol gal pulls like a train again.
 Just need to get the speedo working.

My loom had a weak spot where the cluster of wires coming from the engine meets the main loom on the left of the tunnel. It just seems to hang there causing tension and I had to make a repair there. Might be worth a look.

One other thing to check and I'm basing this on the 500 admittedly is the thick positive cable that goes to the starter motor. The 500 motor has an insulator washer on the stud then a nut and copper washer, the loop on the cable then goes on next before a lock washer and the nut. If you forget the insulated washer the live cable grounds onto the motor casing causing a short but unless you hold the starter button in for hours, there is no fuse for this and all that happens is the cable gets hot...eventually as even 14amps isn't a lot, you'd smell it!
No idea if the 250 is remotely similar.
Also the 250 shares the starter solenoid with the 500 models so check you have the battery lead and starter cable on the correct terminals and haven't got input and output reversed - not sure if the terminals are marked and it is possible to cross them over.

Sounds like as you have the same problem having changed the whole engine, assuming you had all connections correct originally and have still got them correct, that the fault is with another component and on a bike of this age and knowing that Italian wiring of the era was a bit wonky, I would be inclined to change the loom as you suggested. Otherwise it can only be the ECU. The danger of changing the ECU before the loom, is that if the loom has a short it may have damaged the current ECU and may do so with another good one, so I'd change the loom first and if that fails then do the ECU.

I do not have a clue with the X9 bikes as i have never worked on one BUT...you say you have had this engine running on the bench, if so.
How did you set it up to run, what is the difference between the two set ups if it will now NOT run?
Lyn.

On X9 250SL:

front - Fuse collection in glove box- assorted power
           1x Relay fuse switch behind lights - kill switch system and main power
            2x Headlight relays between lights- Headlights

Rear- Fuse collection under seat- assorted power
         1x ignition relay next to battery -controls ignition start up
         1x 30 amp fuse on top of starter solenoid, - cut power to bike

There the only ones on the 250SL
           

Hidden fuse on the relay in the battery compartment?

We had the master one out at front, clean and looks brand new, it opens and closes and your turn the key, so that's working.

Next is relay at the back near battery when press starter motor the relay clicks as it should, still fuel pump has no power as like the CDIis dead or not doing its job.

AS i like this low mileage engine i just bought and put in, i am going to replace ALL Fusses and ALL relays so i know there eliminated also going to plug in the 2nd X9SL CDi i go.

If after that and all els fails, ill stripp the whole loom off and fit another one.

Sounds like a relay problem, check them all especially that 'master' ignition one at the front.