Have you had anyone take a look at your running technique recently?
You may need to rebuild your running technique following the knee surgery.
Yes, the PT gave you a recommendation, but do you have a plan to achieve that?
Is the increase in cadence just to average a 6:30 mile?
You will need to progress to that cadence.

Limited ankle range of motion is a definite impacting factor.
A couple episodes to start taking a look at:
Episode 258: Ankle Mobility-Self Mulligan Technique
Episode 285: Sliding Surfaces; Ankle Range of Motion Case Study Part 1
Episode 285: Sliding Surfaces; Ankle Range of Motion Case Study Part 2

There are several more episodes and Daily MIWod which address ankle rom.
Pro Episode # 57 – Managing Achilles “Tendonitis”

Pro Episode #3 – The Flat Feet Solution

A. Depending on what shoe you were wearing before you may need to scale to a lower profile shoes in stages. Building the strength in your foot is important and required when transitioning to wearing a lower profile shoe.
How are things going with the lower profile shoe?

B. Roop & Jami have a 5 part series within the Episodes tab on the foot and ankle
    There are many episodes and Daily MIWod which address ankle and up/downstream of the ankle, and
    episodes which are running specific.
    Ankle and Foot Webinar: Where the Rubber Hits the Road
C. From the MIWOD List practioner search there are 4 practitioners within 20 miles of DC you can do a
    search for 5, 10, 15, 20 miles of your location.
D. Limited ankle range of motion can impact how/where on your foot you strike the ground. This impacts
     everything up/down stream.