They need to have a path back to the panel (don't pretend you found "ground" on a pipe somewhere), but they don't need to be individual wires all the way back. You can join up grounds, and a #12 or #14 is ok. These are to carry the current from one fault somewhere for the time that it takes to trip the breaker, so they don't need to be bigger than the branch circuit wires and how many you join up doesn't affect wire size needed since we assume only one will be conducting fault current at a time. Connect the ground wires to any junction boxes along the route. You don't need to add additional junction boxes just for the grounds. The ground should follow as closely as practical the route of the hot and neutral on each circuit. If a fault current has to make a big loop (hot from the panel, fault somewhere to ground, and a different path on the other side of the house back to the panel) the breaker trip time can be extended because magnetic field effects limit the current. You want a very large fault current for a very short time to trip the breaker fast, not 40 amps for a long time heating things up before the breaker trips.

At the main disconnect (typically the main panel), ground and neutral are bonded together and using the same bar for neutrals and grounds is permissible. In other places, the grounds and neutrals must be kept separate all the way back to the main disconnect. You need a neutral bar isolated from the grounds. What you describe would be fine if this were the main panel. However, it seems like the main disconnect is not either of the Siemens panels are subpanels. You are right, the neutrals should be on their own bar electrically isolated in that panel from the ground. As for the pipe, if the interior piping is copper (regardless of the external connections), it needs to be bonded. This isn't providing an additional ground (like connecting to the incoming metallic pipe would), but providing safety in case some live wire should come in contact with the interior piping that would engergize all your faucets ,etc...

It's a hazard and so blatantly wrong, that if you're even considering it you have no business even taking coverplates off. 250.130 would be a good place to start but it's probably in violation of a ton of other articles as well. About the only time you can use the grounded conductor to carry the equipment ground is a few grandfathered cases for stoves and electric clothes dryers.

The third wire ground ( the green wire) is all about completing the circuit to ground at the voltage supply end (the transformer) to insure that the breaker will trip if there is a dead short in the wiring (like if a rat chews the insulation off and bare wires touch) or if there is a lightning spike before some appliance gets fried or a fire starts.