Hello there! I used to work at the VA as a veteran service rep, so I wanted to try an help make your claim process a little easier. :)
Do you have an eBenefits account and a MyHealtheVet account? If not, I'd recommend getting both. You can file for VA benefits via eBenefits online, and, with MyHealtheVet, you can view any and all medical records and lab reports you've had done at any VAMC. It comes in VERY handy when filing for benefits.
From what you said in your post, I'd recommend claiming the following conditions.
Bilateral knee pain
Bilateral ankle pain
Back pain
Sinusitis
Headaches (secondary to sinusitis)
Anxiety (secondary to bilateral ankle pain)
Note: Explain how you were separated for a PT failure, and how this condition not only ended your military career, but it has caused you undue stress at work and home because you aren't able to complete daily tasks without it causing pain. The more information about how this condition affects your life in a negative manner the better.
Here's the rating criteria for both Sinusitis and Rhinitis. Claim the one that best matches what's in your military records, and then claim headaches as a secondary condition to it.
6514 Sinusitis, sphenoid, chronic.
General Rating Formula for Sinusitis (DC’s 6510 through 6514):
Following radical surgery with chronic osteomyelitis, or; near constant sinusitis characterized by headaches, pain and tenderness of affected sinus, and purulent discharge or crusting after repeated surgeries...50%
Three or more incapacitating episodes per year of sinusitis requiring prolonged (lasting four to six weeks) antibiotic treatment, or; more than six non-incapacitating episodes per year of sinusitis characterized by headaches, pain, and purulent discharge or crusting...30%
One or two incapacitating episodes per year of sinusitis requiring prolonged (lasting four to six weeks) antibiotic treatment, or; three to six non-incapacitating episodes per year of sinusitis characterized by headaches, pain, and purulent discharge or crusting...10%
Detected by X-ray only...0%
Note: An incapacitating episode of sinusitis means one that requires bed rest and treatment by a physician.
6522 Allergic or vasomotor rhinitis:
With polyps...30%
Without polyps, but with greater than 50-percent obstruction of nasal passage on both sides or complete obstruction on one side...10%
It's also a good idea to scan any and all documents regarding each condition into a PDF file, and upload them with your claim.
I hope this helps get you started! Please let me know if you need any help!