1. Yes, you can take out the manifold guts and run water to all the pop-up locations at once.
2. I'm not aware of any type of replacement flush vent from Caretaker, but maybe others here have some ideas. (bump)
If you have a variable speed or 2-speed pump and leave the original pop-ups in place, you can run on lower speeds without the manifold and all the pop-ups should stay in only a slightly elevated position. You'll get more uniform distribution of the water. This is beneficial when you are running a heater, though you get mostly the same result with the manifold guts still in place. Most likely, the pop-ups won't rotate at the lower pump speeds. And of course, they won't do much "cleaning" at the lower pressure.
If your goal is for chemical distribution, be careful that concentrated fluid coming out of the pop-ups to the same small area on the plaster may not be a good idea over time.