Pilates is great, I used it a lot to strengthen core, I went to local Pilates classes at first, but they were expensive and we never seemed to move on, so I bought this and did the exercises at home.
I also do a lot of stretching, I had really bad PF when I first started running, typical beginner's mistake, too many miles too quickly with no stretching. I built up a routine for all over stretching, but particularly, calves and feet. The Inverted V stretch is great for hammies, calves and back all in one.
I also wear orthotics permanently. I'm tall and had back problems all my life. A few years ago, I ruptured tendons in my feet and had to undergo surgery. When that was over, I was prescribed orthotics which corrected my posture and since then, I've been pain free.
I do think that it's important to build up a good base of mileage, but as someone said, mixing in speed. My weekly runs include LSR (at slowest speed), tempo sessions (number of repetitions of shorter bursts of speed with recovery,) at full effort, almost gut-busting, and then steadies which are shorter than LSRs, but run at a faster and consistent pace.
I really like HR training, I got into it last year following the January challenge and for whatever reasons, make more progress on that than going by pace alone. I was recommended the John L Parker Jnr book, "Heart monitor training for the Compleat Idiot".