As you correctly state, the Ford 289 small block is externally balanced. This simply means that when the small block was designed, there was not enough space for sufficient weight on the crankshaft counterweights to balance all of the mass of the reciprocating parts (rods, pistons & rings). So they have to take care of the remaining imbalance on the flywheel, harmonic balancer and the hatchet. Therefore, an originally built motor must be balanced with the crankshaft, flywheel and harmonic balancer assembled together on the balancer machine.
Sorry, I do not know the proportions of the imbalance between the damper, hatchet and flywheel that you've listed. I'm not sure it matters to the guy doing your balancing as long as you make sure you've physically got correct and original parts. Bob mentions those numbers here (presume you've read this article?) : http://www.fordsmallblock.com/PDF/SmallBlockV8Balancing.pdf
Your last point is correct - fitting the pistons, rods and rings brings the whole lot back into balance.
I see you're in the UK. I recently had a 289 motor balanced by Steve Smith of Vibration Free (near Bicester) and from driving the new motor, it was an excellent job. He has balanced many Ford 289 motors (HIPO and non HIPO) and I would recommend him.
Hope that is some help.