I'm connecting up all the wires now to the megasquirt, one wire on my V3 diagram is labeled Ignition module/output.

As i'm only running fuel on the MS and using the stock honda cdi ignition box, presumably i connect this wire to the cdi box, but to where?, tacho feed or coil feed?

Ash.

Do you mean you're configuring the MS to only run fuel, with no ignition map? if so then you can simply ommit the wire, or hide it with the end heavily insulated.
Or are you running it a la an edis set up where you use the ignition module controled by the MS?

Yes fuel only with the ignition run using the honda ignition module & coils, surely the MS will need a feed to orientate itself alongside the ignition?

All it needs is a trigger reference to work, such as single tooth, or spark event. This usually comes from a trigger wheel to also give the rpm, but can be formt he igntion system if that works on its own. Other than the trigger signal, there is no need for the ms to even know there is an igntion system. The input for the MS will likely be on the tach input/pin. Best bet is to have read throuhg the megamanual again at the igntion options and trigger inputs to see what you're using.

Thanks, had another look at the diagram and it was staring me in the face! I'll use a Tacho input as a reference.