Here's what I have done when I get machine work done on a std. rebuild.
Hot tank and magnaflux the block for cracks. That's always first, so you know you're starting with a good block.
Bore or hone the cylinders, depending on what they need.
Align bore the mains to ensure it's all true and to size.
Size and inspect all the rods. I also have the shop press the new pistons on at that time.
Check the crank and turn as needed.
Clean and check the heads. New valves or refinish the valves. I always use SS valves if they don't have them in the heads, and new hardened seats if they don't have those. Check all the springs, and do a valve job on the heads. New guides and seals.
Once that's done I have them flush the block and install new brass soft plugs, and all the threaded plugs too.
I also have the shop press in all new cam bearings.
When I get it home I fit all the rings to the cylinders they will go in, then install them on the piston/rod for that cylinder. I plastigauge all the bearings, just to double check the shop's work and then install all the new main and rod bearings.
Then just reassemble the rest the pieces, cam, oil pump, lifters, heads, etc, etc.