Fine work there!
Aluminium inserts for PB – I'll try to remember that.
That flywheel's spot-on.
I don't think you've had to lift the motion excessively. The top of the firebox is a bit on the thick side but not that much above the barrel, and the cylinder saddle will compensate for some of its thickness anyway.
I may be mistaken but I think the engine in the photo behind yours is a single-crank compound. Are you following that or making a single-cylinder engine? If the latter your cylinder-block will be proportionately a little bit less tall.
I don't suppose you are the first to be caught by things like someone putting an axle in the way of the fire-door. They would! Many traction-engines have either the axle or a motion-shaft not actually in its way but above it, and some seemed to have been designed to make access right awkward. At least yours is below the door.
I've certainly fallen into my own design traps many times. There are plenty of bits on my steam-wagon that are second, third… mods to overcome mistakes I had not foreseen maybe 10 weeks – and often years – beforehand.