Your 2-inch thick cabinet bottom and poorly routed PEX lines are classic examples of RV manufacturers prioritizing cost over space efficiency. These issues can be addressed through cabinet modification and PEX rerouting.
Chassis battery drain is typically caused by parasitic draws from electronics, clock radios, or converter issues. Dead outlets near dinette/kitchen suggest a tripped GFCI or loose connection in that circuit.
Your comprehensive rebuild plan is solid, but focus on structural integrity preservation, proper moisture barriers, and weight distribution. Critical areas include electrical safety, plumbing rerouting, and maintaining slide-out mechanisms.