The valves are fine. It's totally up to you what you want to do with them.
If you left them alone they'd work. But you don't want it filling up with water.
You could always get a second box of the same size, put it over the existing box to make it ground level. Some digging would be required. Just beware of the wiring.
The boxes are open on the bottom. Or just rearrange the existing box by digging it up.
Got the valves dug out so the tops of the diaphragm covers are all visible and the drain valve is now freed up. I noticed a small leak on the top diaphragm cover of one valve but tightening the phillips screw eliminated the leak. So no leaks now. Later this spring I might take your advice and dig up the whole box and reset it so it's a bit more at ground level. Good to know about it being open on the bottom. I kinda' thought that was the case but wasn't sure. The wiring is all exposed now so shouldn't have to worry about accidentally cutting through a wire. Now that I understand a bit more about the box, digging it up shouldn't be a big deal, if I decide to do that.
Tested the system and all seems to be working just fine. Only had to replace one head (so far) that was broken off down low when I managed to run it over with the riding mower. Probably replace a couple others, too. We have mostly Rainbird impact heads and I've just been replacing them with the Orbit Voyager II heads as they start to act up. One of the Rainbird impact heads is set to turn 360 degrees and I don't know if Orbit makes one that does the same. If not, I'll just leave the impact head in there for now.
Thanks. Sure appreciate your help.