I have decided to leave the Joe rig and call it finished. This is mainly because there are numerous problems that are too much hassle, I could have just started a new rig instead. Even with all these problems I feel the rig has been somewhat successful because it has the key features I initially was after; reverse footlock and stretchy limbs. I also ended up finally understanding why I was have problems with painting weights, it was the reason I ended up rigging the entire eel. The stretchy limbs work well and look awesome, I just wish I could have sorted out the torso and added set driven keys for the hands. I made up for the latter by making a separate hand rig to demonstrate I know how to create set driven keys well. I was never sure what caused the fingers on Joe to bend incorrectly but I am guessing it could be the weights, that is not a definite answer though.
Below are some shots of the rig posed, these are not the best or most interesting poses but they show the rig in action.