Possibly your shin pain is shin spints and your ankle biomechanics aren't brilliant which would have predisposed you to your knee injury. May be worth looking into a podiatry referral - but best to see a physio first to confirm that one.

The meniscal injury is often coupled with a ligament injury of the MCL and sometimes the ACL. By the time your meniscal injury has healed your MCL should have too - but if your biomechanics are off then this could slow the process.
During arthroscopy they would have seen in your ACL was overly damaged so we should be happy that this is ok.
With the clicking and posterior pain it's possible they missed a bit of Wikipedia reference-linkmeniscus in one of the areas near the back of the knee - heres hoping they haven't.

Based on all the possibilities based on your symptoms make sure you get stuck in with a good sports or musculoskeletal physio.