Welcome to the forum. Where are you located? That can make a bit of difference in construction. In my fair city of Houston Tx, that shower liner can't have nails within 12 inches of the plywood, so that is one reason for it to go. And its already 8 yrs old. If you are dead set on keeping it, I would do a flood test first. You want the pan to hold water for 24 hours at the height of the curb. Acutally the tiles that would be laid on the curb, so no nails in the liner within 2 inches of curb height. Taking the pan out and replacing it is a fairly inexpensive procedure, it just takes some time.
I read your waterproofing method is planned on being sheet plastic behind CBU. Did you consider a surface applied liquid membrane or sheet membrane such as kerdi or noble? I am not a fan of plastic sheeting behind CBU. They just take longer to fail IMHO which is why I am a Kerdi fan.
I like to tile the floor after the walls are tiled, some do it differently, but I would think the vast majority tile the floor after all the prep work is done. The rest are half-vast.
The trench occurs in a properly installed shower for a few reasons. Since you shouldn't put nails through the liner, how would you secure the bottom foot of the CBU? The cement floor of the shower holds the bottom of the CBU from swaying in the breeze. This is where I get to preach again. You can see how the cement base of the shower can hold water. That water migrated up your old drywall walls and destroyed them. If you build your new shower walls out of CBU with plastic sheeting behind it, the water will migrate up the cbu. It would make sense then to have the waterproof layer right under the tiles and above the cement base, no?
Some minor plumbing changes to the drain, a new faucet and you're in business.