How can I complete these repairs to my sprinkler system?
Well, I think you have some remodeling of your sprinkler system to do. Here are some things that you need to think about.


There needs to be an anti-siphon type valve on each controlled sprinkler circuit. 
These anti-siphon valves need to be mounted at an elevation that is 6 to 12 inches above the highest level of the sprinkler heads on each circuit. Not in a box buried under the ground.
Since all of the controlled valves will feed off of the same pressurized main water line it is convenient to install all of the valves at the same elevation.
If you want to hide the valves then build a wood cover that is above grade to hide then and blend in with the side of the building structure. 


So if you understand the above most of your questions become moot. Pull that box of the ground and toss it away. Then re-pipe the main water feed line to above grade and create a manifold arrangement that can feed to the number of anti-siphon valves that you need (number of controlled sprinkler circuits). The manifold is best placed closer toward the building foundation. Then re-pipe the various sprinkler circuit pipes so that come up right in front of the manifold connections. The valves will affix above. When it is completed it can look something like this:



or like this:



The advantages are many. It is much easier to repair and replace things that you can get to. The anti-siphon type valve, properly deployed, is the tried and true method to provide the isolation between the pressurized potable water service and sprinker circuits. Placing your control valves high like this is also an advantage if you live in a freeze climate zone where it becomes necessary to use pressurized air purging of the lines to clear out all the water before winter. The air can be applied to each circuit at the control valve. Lastly your low voltage control wiring is above grade where is stays much dryer and less chance of wiring corrosion.