Okay, this is a complex situation with a lot of historical baggage. You've accurately identified several code violations and potential safety hazards. Let's break down the issues and discuss solutions, keeping in mind the constraint of not replacing the underground feeders. I'll reference the NEC as a guide, but always confirm with your local AHJ (Authority Having Jurisdiction) for their specific requirements.

Core Problems



Multiple Grounding Electrode Systems Connected by Ungrounded Feeders

This is the primary problem. Each building effectively has its own grounding electrode system (rods) but no equipment grounding conductor (EGC) connecting them back to the service. This creates a situation where fault current cannot effectively return to the source (the SE panel) to trip a breaker. This is VERY dangerous. Faults can energize conductive surfaces and create shock hazards.

Reliance on Earth as a Fault Current Path

The grounding rods are not intended to carry fault current. They're primarily for stabilizing voltage and handling lightning strikes. Relying on them for fault clearing is extremely unreliable and dangerous.

Subpanel Neutral/Ground Bonding

Bonding neutral and ground at subpanels is a recipe for circulating neutral currents through the grounding system and creating objectionable currents. You've correctly identified that it's only sometimes correct in the historical context you've laid out.

Ungrounded Feeders (Lack of EGC)

This is the root cause of many of the problems.

Analysis of the Current Situation, Building by Building


Garage (Service Entrance)



Status

Good to have the SE panel properly bonded with rods and a neutral-ground bonding jumper.2.

Main House



Issue

Fed by an ungrounded feeder from the Garage SE. You say there is a rod and a water pipe ground, but you have not described how these are connected to the electrical panel or the equipment in the house. Having a separate rod and a water pipe ground is useless without a properly sized EGC connecting them back to the source of power!



The Fix

This is the most difficult to answer without knowing the full details of the "water pipe ground" and rod. The bare minimum is a properly sized grounding electrode conductor (GEC) from the panel to the rod and water pipe. But there is no way to make the situation compliant without digging up the feeder and installing an EGC.3.

Shed



Issue

Fed by an ungrounded feeder. Has rods, and the neutral/ground are not bonded (which is currently correct).

The Fix

Similar to the main house, you need a properly sized GEC running from the subpanel to the rods. This makes it the most "safe" that it can be without an EGC in the feeder cable. But there is no way to make the situation compliant without digging up the feeder and installing an EGC.4.

Pool



Issue

Fed by an ungrounded feeder. Has a rod plus a concrete encased electrode (CEE), which is good. Neutral/ground is bonded (incorrect).

The Fix

Remove the neutral-ground bonding jumper in the pool panel. Ensure the pool equipment, rebar, and fence are all properly bonded together and connected to the equipment grounding bus. While not code compliant, the CEE and the rod improve the likelihood that a fault will ground, and with all of the pool equipment bonded together, it limits the opportunity for differential potentials to develop. There is no way to make the situation compliant without digging up the feeder and installing an EGC.

The (Unsatisfactory) Solutions, Given the Constraints

Given the hard constraint of not digging up the feeders, the solutions below are about mitigating the danger, not achieving full code compliance.

These solutions are NOT ideal and DO NOT eliminate the shock hazard. They are compromises.

Here's the GENERAL approach, broken down into steps


Properly Size Grounding Electrode Conductors (GECs)

At each building (Main House, Shed, Pool), you MUST install a grounding electrode conductor (GEC) from the grounding bus in the panel to the grounding electrode(s) (rods, CEE, water pipe).

This GEC must be sized according to NEC Table 250.66, based on the size of the service entrance conductors at the Garage (SE panel). Do not undersize these GECs. This is crucial for minimizing voltage potential differences between the structures.2.

Ensure Rods are Properly Installed and in Good Condition

Driven deep enough, spaced properly, and connected with appropriate clamps.3.

Remove All Subpanel Neutral/Ground Bonds

Except at the service entrance (Garage) panel, the neutral and ground must be kept separate. This eliminates the possibility of neutral current flowing through the grounding system.

This means you MUST remove the neutral-ground bonding jumper at the Pool panel.4.

Bonding (Especially at the Pool)

Ensure all metallic parts that could become energized are bonded together with a solid copper conductor. This includes: Pool pump housing Heater housing Metal conduit Rebar in the pool deck (as you mentioned) Metal fence sections within reach of the pool Any other exposed metal items5.

GFCI Protection

As much as possible, provide GFCI (Ground Fault Circuit Interrupter) protection for circuits serving outlets and equipment in the Main House, Shed, and especially the Pool area. GFCIs will help to detect and interrupt ground faults, even if the grounding system isn't perfect.

For the pool, GFCI protection is required by code for many (if not all) circuits.

Important Considerations and Caveats



THIS IS NOT CODE COMPLIANT

I cannot stress this enough. You are working with a compromised system. The lack of an EGC in the feeders is a fundamental safety flaw.

Potential for Objectionable Current

Even with the neutral/ground bonds removed from the subpanels, there's still a possibility of objectionable current flowing through the grounding system due to the long distances and the impedance of the earth.

Professional Inspection

Strongly recommend having a qualified electrician inspect the entire system after you've made these modifications. They can perform tests to verify the grounding system's effectiveness and identify any remaining hazards.

Future Upgrade

Make a plan to eventually replace the underground feeders with properly sized cables that include an equipment grounding conductor. This is the only way to truly make the system safe and code-compliant.

Disclosure

If your friend ever sells the property, they MUST disclose the electrical system's deficiencies to potential buyers.

Local Codes Prevail

Always check with your local AHJ for their specific requirements. They may have additional rules or interpretations of the NEC that apply to your situation.

Specific Questions You Raised



Removing the Bonding Jumper in the Shed Subpanel

Yes, removing the bonding jumper was the correct thing to do given the existing ungrounded feeder. With no EGC, bonding neutral and ground creates a parallel path for neutral current.

In summary: This situation requires a pragmatic approach. While you can't fully fix the underlying problem without replacing the feeders, you can take steps to mitigate the hazards and improve the overall safety of the system. The key is to focus on bonding, GFCI protection, and ensuring a robust grounding electrode system at each building, all while remembering that this is a temporary solution and that replacing the feeders should be a high priority for the future. Consult with a qualified electrician and your local AHJ before making any changes. Flag for review