Having recently fitted a new engine due to gearbox issues (jumping out of gear etc) We want to be certain the adjustment of the cable for the new gearbox is correct before we start etc. Is there a correct way of dong this? Or just keep adjusting the cable out at the engine end until it will sufficiently select 1st, make sure it will still select neutral and the rest of the gears and thats it?

There isn't really much to set up, clamp the outer sheath so it gives you a good range of adjustment length at each end.
Connect up the gear shaft end and the gear lever/paddle end and then fine tune the rose joints on the ends to put the lever central or paddles perpendicular with the steering column.

As long as the lever/paddles are correct and the gear change arm is vertical then all is good.

The throw of the gear selector is dictated by the gear lever or paddles.


The other thing to think of is the throw length. The shorter the throw of the lever/paddles the more force is required to shift gear.
ideally you want the cable mounted as close as possible to the pivot points on the lever/paddle and gear shift arm without it putting too much strain on your arms/hands/fingers. This would give you a really short throw but require more force than if they're mounted further from the pivot

as said
as lond as the fitting allows the max moment of the lever at the gearbox end in a free and smooth action thats it, the rest is in the gearbox

I suppose when you think about it, on a bike no one is taking this much care to change gear with their foot?

Our concern was not selecting the gear fully/being properly home etc and thus causing wear to the dogs in the box.

A problem I found I have is sometimes I don't pull the paddle correctly, just a little fairy pull on it and it doesn't engage the gear fully or something, halfway through the revs or whatever it'll then jump out of gear. If I give it a full, aggressive pull, no problems