Kevin, I reviewed MPandC's sticky but that was a while ago and probably should look at it again.
I looked over your bed side pictures and there are definitely some similarities. In my case the angles were basically rusted away and tended to take the bed side with them (at least in the front and back). My fender mounting areas were not as bad as yours.
The driver's side door is going to be basically a full width inner and outer patch panel so making sure that I know where the bottom needs to be before I cut off both areas will be critical. My current plan is to make a carbboard template that I can bolt in place on the inner panel (because its flatter) to idenitfy the bottom edge location but I am open to suggestions.
