As a followup, with help from other forums and using example letters, I sent my own letter disputing the charges and why. I politely told the company hired by the rental car agency that I would only speak to them by email. Along with my letter I enclosed my deductible via cashiers check and sent it signature required.
Yesterday I received an email from the rental car agency saying that they had received my dispute letter and deductible. They have asked the company they hired to remove all other fees and charges and accept my deductible as payment in full. They also state they will pursue no further collection of monies from me and the case is now closed.
Just goes to show you what happens when the little guy fights back against "anticipated" loss of use and diminished value. These companies are allowed to charge these junk fees but failed to give me proof of how they came up with the dollar amounts. Hopefully this helps someone else to do the work and take the steps to fight back. I'm glad I did. Turned a bill of over $4,000 into $0.