Zero deck height is machining the deck surfaces of the block level with the top of the pistons @ TDC, and obviously parallel with the crank centreline and square with the bores. You can go below that height and rely on the head gasket to provide clearance to the head too, but that's usually only done if you're chasing every last bit of CR (the compressed thickness of the gasket needs to be taken into consideration when calculating CR as well).
Bear in mind that probably means you'll lose your engine number stamping too so ask the shop if they can restamp it again afterwards?
A dual plane air gap manifold almost certainly won't fit below a standard Torana bonnet either so if that's the way you're going, don't bolt the bonnet on and just slam it down without checking!
Sooo... I'm guessing you don't have a lot of experience assembling engines?
If that's the case I'd at least get the shop to install the new cam bearings for you (and clock the oil holes correctly with the new oiling mods). And get them to hot wash the block and heads thoroughly before giving it back (and even then don't trust them to have gotten everything out, ESPECIALLY FROM THE OIL GALLERIES).
Also make sure you grab some Plastigauge or similar to check the bearing clearances. And there's a whole procedure for installing the rear main rope seal if you actually want it to seal (youtube is your friend there, COME Racing have done some good videos on the subject). Remember to check the crank end thrust, and make sure to continually check for binding as you tension the caps, if the crank locks up you've got a bearing problem.
And don't forget to check the ring gaps and side clearances, if they need filing and you don't do it they will likely break on the first run (if they didn't break on install), and clock the ring gaps on opposite sides of the piston and not on the thrust side of the bore. And double-check they've fitted the conrods in the pistons the right way around (so the oil squirter grooves point toward the opposite bore from memory)?
And... probably a hundred and one other things I haven't listed above! It's been a few years since I rebuilt one myself but I doubt they've changed much...