Whew! That is a big block diagram! Some tips, don't hide the labels of the terminals on your block diagram.
Also use block diagram cleanup to shrink the size.
Before creating a monster size program, start smaller. Create a VI that gets one motor to work. When you've done that, then you know you have some working pieces to build on.
When expanding, start thinking in terms of modularity. Don't create 6-7 times the code. Think subVI's that do one thing that can be repeated 6-7 x for each motor/pump via For Loops. Think arrays. Don't create multiple nested True/False cases where the only difference is a constant output. Think in terms of calculations and logic that would let you work with multiple case case structures, or code that can calculate what that constant should be.
Control Applications imply a state machine architecture where you sequence yourself through a series of steps and decision logic can determine when to move to the next step, stay in the same step, or even return to an earlier step.
Don't create monolithic applications that are hard to modify or expand on.
Write your documentation first. Create flowcharts on paper that define your series of steps. Then throw away what you have and start over.
