"The old tub sat over a 1ft by 1ft hole in the slab, and I'm not sure about how the plumbing should be handled. Do I plumb it up and fill the hole with concrete?"
Yes, the tub dap-out must be filled before the shower pan is formed.
"Where should the lip of the shower drain be set in regards to the existing slab? "
On a custom tile shower the drain can set anyplace just as long as the shower floor slopes to it.
"Should the slope to the drain be made before the liner goes down?"
No. The shower pan and flange type shower drain will install first.
"How do I keep the mortar out of the weep holes?"
Very carefully! You will have to ask a tile man that question. Our work's done when we form the pan, set the drain and install the shower valve.
"If someone has pictures or a link to this information it would be greatly appreciated."
Click on;
Mortar Bed Shower Floor for Tile Showers for pictures and instructions.
Good luck on your project, Tom