Building a bike: timelapse

[rustyrider]

I'll be able to start work on the engine.

Have you checked the piston rings in the bores?  Take them off the pistons, fit them into the bores then check the width of the gaps with feeler gauges.  If the original problem was low compression it could have been the rings or could be valve seats.  Fit the spark plugs, turn the head upside down and fill the combustion chambers with a liquid (it's one of the few useful things you can do with diesel) and see if it dribbles out of the ports.