engine last in my opinion .... its easier to work in the engine bay on the fiddly stuff with no motor
and depending on what lifting gear you have... try with the gearbox attached (if it can be done on a Commodore surely a HJ would be possible)

Finish the engine bay with all firewall stuff done. Put the motor together with clutch and bellhousing on, and exhaust manifolds on but leave the water pump and alternator off. Leave radiator out. You'll most likely have to leave the bonnet off. Lift it up high and drop it straight in, you might have to tilt it or do it angled. Just use thick removalist blankets over the nose and radiator support and over the guards. Try and use an overhead hoist or chain block rather than a crane. You might have to use an engine leveller that tool shops sell, engine will hang off the head accessory bolts. You can use longer bolts and nylon spacers so that the leveller chains don't tear the paint off the heads around the bolts.

Where it can be tricky with a nice and newly painted engine bay is getting the mounts to line up without scratching. Not sure how you do that, maybe duct tape over the mount posts on the rails?

Make sure you setup the clutch before it goes in with an old input shaft, so that the gearbox goes in easily once the engine is on its mounts.