I like your plans, it is similar to an idea I had about making a Solsylva CNC with 80/20 extrusion. In the end I went the safe route and am building it like the plans on the CNC Routerparts & Fine Line Automation site. Sawdust (routerdust??) falling onto the cold rolled steel rails and jamming the ABEC bearings was a concern I have and mounting it on top like you have would alleviate that problem (along with a dust shoe).
As for the drill rods and couplers, you won't need those since you are making your own design. Their plans still call for the drillrods and lovejoys even though they now offer a helical shaft coupler. The drillrod also gives the ACME rod a little more usable length, but since they sell ACME in 3 ft and 6 ft lengths, you won't have to worry about that for your Z-axis.