You can petition the court to commute your PD indemnity. There will be a mandatory 3%/annum deduction to bring that to 'todays dollars'. Then the AA fees will be deducted.
In a lump sum payment/C&R including the medical, the AA fees will come from the total amount....that medical money should, may have to be, deposited in a interest bearing account for your injured body part ONLY. Not to be used for moving expenses, or bills etc.
The stips were in your best interest. Getting the rating agreed to was important. Taking the time to evaluate your furture medical needs is also a good idea. You never know what the potential need is for additonal treatment.
You do have the ability to file to re-open this claim for new and further disability within 5 years of the org DOI...that too is in your favor. Your AA is looking out for your best interests here... he could have C&R'd this claim, taken the fees and simply walk away.
From the info you provide here...looks like about 13K net in a commutation on the remaining PD (?). Not bad, but understand that does not go far these days.