Day of off work has proved fruitful. I managed to get the column to fit correctly and clear the valve chest nuts by making some 7BA 1/2 nuts from 8BA ones - fiddly

This still didn't give me enough clearance and the column was getting pushed backwards and not sitting correctly, so I thinned the valve chest cover and reduce the little bosses on it until it all fitted together. Then onto milling the clearances spaces on the top of the column for the eccentric and crank
With the column now bolted to the base I started to put the engine together and this one is going to take a fair amount of fettling. The crosshead guides are hitting the spacers at the top of the stroke and it feels like the piston (or something) is hitting at the bottom of the stroke.
Time to call it day for today!