I think most of these questions would be better answered at the John Bridge forum. www.johnbridge.com. Check it out.
In the meantime here is some of my .02.
Consider that you'll need to put ply and hardi over the plank and what it will do to your floor height once installed. I'd consider pulling all of that up and lay brand new 3/4" ply with 1/4" hardi over that. The tub gets mortored in around the drain area and yes you lay the mortor right on the ply. No Hardi under the tub. If you use ply it goes over the mortor under the tub to stop the mortor from adhereing to the tub. Yes you should cut your holes for sewer services to be installed later. Consider the size of your toilet when doing this.
However you'll likely need to run your joist type, span and flooring type through the deflecto meter on the John Bridge website to see if maybe you need to sister some joists and or add additional layers to the floor to stiffen it.