Trail shoes PLUS debris gaiters on NDW if you don't want to keep stopping to get bits of stone or stick out of your shoes. If you CAN do a couple of recces do so (it splits nicely into two sections, Farnham to Dorking, Dorking to Knockholt Pound) then do so as there are one or two bits where it's possible to go wrong (done it, seen others do it) even with the extra markings on the day.
Box Hill and the 2-3 miles(?) after that are tough, but it does get easier again after that section. Accept that you'll walk up Box Hill.
This was my first 50-miler, back in 2012, and I really enjoyed it.
Agree that it's likely to by posterior tibial. Unfortunately the tendon, which wraps around the ankle bone, has a very poor blood supply so healing is slow. There -are- exercises that the physio can get you doing. Definitely get this sorted sooner rather than later or it will take much longer.