To line up the crank pin holes and get them the right distance from the axle, I have created a little jig out of 1/16 x 1/2 inch brass. Using relatively heavy material like this should keep wear to a minimum, at least long enough for two or three engines.
The jig is pointed at the tyre end so I can point it at the midpoint between two spokes. I suppose if I’d been cleverer, I would have made it wide enough to point at two spokes. If I’d been downright genius, I would have etched it with the other parts.
A test run with a throw-away crank pin and the proof of concept driver showed it works fine.
Pembroke:87 
How does the jig index the distance? Perhaps with a peg to slip into the wheel hub? Or maybe a circular groove the radius of the wheel rims? or ??? Curious minds . . .
Similar question: how did you make the jig precise enough? or is this a case where making them all the same is more crucial than making them a precise distance from axle centre?
Oh, here I thought that was obvious! The wheels are all already on their half-axles!
I was careful when setting up the jig, but you are right: the key is to get all four wheels the same.