You can let it run without the guts in. It will just allow all zones to get flow at the same time.
Try to make sure that nothing gets in the open holes where the pop ups are missing.
I would keep an eye on the cup screen to see if it's continuing to clog. Maybe just leave it out for now.
I would switch the actuator switch back like it was.
One last question, hopefully, the Caretaker pop ups in the spa have been removed, but there’s no flow. There was a bit initially (some bubbles) but nothing now. I did notice that when I took the Caretaker Head unit apart, four of the five “discharge” pipes drained, but one stayed full. Any correlation? Any ideas on how to get flow to the spa pop ups.