need help.

bought a bike that had a dodgy wiring harness which had an intermittent fault on the fuel pump circuit.  It ran but I opted to replace the harness. 

The bike is a non abs model, I replaced the harness with an ABS model. 

Everything works, lights, speedo, etc.  The engine cranks, the fuel pump pumps ... But no spark. 

Is there something I need to blank on the ABS that may be preventing the spark?

AM I missing someting

It shouldn't matter if it's ABS. Nothing related to ABS influences ignition.

There are a few minor differences that evolved over time. One is in the fuel pump/fuel level area but seeing you have a running pump I would say that's not the case and the other was the connector to the instruments but considering the fuel pump is OK then that instruments issue should also be OK.
There is a small trap in that in the right side cover area there are 2 plugs that are the same. one is for the gear position indicator and the other is an ABS plug and strange things happen when they are swapped. It would pay to check that colours are the same and match in the plug and socket but I cant see it being an issue.  As Duck said there is no connection between the two.
What I would suggest first is to reseat the plug on the ignition control unit which is under the top frame tube just behind the head stock and the same for the engine control unit which is under the seat in the compartment of the tool tray.

There is one place to check that well could be the problem. The cable from the ignition sensors at the front of the engine and the cable from the right side ABS modulator have also the same type of plug and are in the same area (right side about midway under the fuel tank) as there is no ABS then the socket for that modulator should be vacant and may get mixed up with the ignition sensor cable. Have a look it could be worth the look.

FYI: ABS connectors are blue, others are black.

Wiring colors at connectors should also match up.

I replaced my full loom earlier this year is I've been here.

I was told by motor works that it is critical to get the right loom for the bike and not mix them up.

A lot of small changes were made year after year.  I was told that the abs loom has a lot of differences from the abs loom.

Ones you can't see as the connectors might be the same but the wires are not.

Mike

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I call pantload on that.

Aside from the ABS, front turn signal light wiring (which is still the same color wires) and possibly instrument cluster connector, all K100s' wiring are the same. They all employ the exact same ICU, L-jet and every other electrical component.

The only other difference is the pre-emssions K100s that had an additional connection for the idle vacuum switch on the early ones - which still wouldn't be an issue.

The 85s and earlier have some different connectors for the FLS, ignition switch and GPI but I'd still be able to get any K100 to run on any other K100's main wiring harness.

The only one "big difference" that would be "critical" is between the RS and LT from 1989 to the end of the LT production because RS is Motronic and LT L-Jetronic. Other than that you need to go back to 1985 before there is any change.

The guy at Motoworks probably knows that if you take into account the naked bikes and the ABS models there is probably 13 different harnesses but in reality only 3 that are essentially different.

All in all the spare parts people know that there are 87 different part numbers for a particular type of item and that means to them that they should always be replaced with the correct part or a thermonuclear explosion will destroy the car, dealer and factory all in one hit. Spare parts guys are the last people to ask about things that are interchangeable.

in reality only 3

Exactly:

1) 85 and earlier
2) 86-on (ABS or non-ABS)
3) K100RS4V (which is a different generation K)