Welcome to the forum, Nic.
1. If you set the drain with plastic nubs on the subfloor, I think the flange sets 3/4" off the subfloor. You really want it at least that thick. If you're measuring up from the top of the lath, that may be where you're losing the 1/4".
2. No adhesive needed. When you set the mud on top of it, it'll flatten out. To make installation a little easier, heat it up with a hair dryer to get it to lay flat. Do so before you attach it to the studs, and before you cut it at the curb.
3. It's not unusual to use three 2x4's for the curb. By the time it's finished with tile, it'll be 5 1/2" tall, give or take, but then you would add some height to the floor, so the curb doesn't look so tall. You can stick with just two 2x4's but the finished curb has to be at least 2" above the drain. You may not be able to do that once you have the pre-slope, liner, and mud bed in place.
Don't use cement board on the curb. It's the cause of many failures that we see around here. I don't know anything about the pre-formed curbs to give you any advice on that. My advice would be to make the curb out of mortar mix. You would do so by forming the lath over the curb after the liner is in place, then put mud over the lath and shape it as needed.