I HATE milestones. I mean, I think there should be something -- children should be walking by the time they turn 2, saying a few words by the time they turn 3, reading by 7 or so. If they consistently avoid eye contact, get them checked out. And that should be IT.
In other words, if a child is truly significantly late on something, parents should know. But it's hard enough to parent a toddler without this added, pointless anxiety. And that's what milestones provoke.
Your son sounds absolutely fine -- like a truly wonderful little boy. He IS going to start running at some point, and when he does it'll be a combination of a heart attack and a fitness regime for you -- because toddlers quickly get FAST. Enjoy your ability to catch him while you still can.
My own son was late with just about every milestone there was -- including but not limited to running. He never did anything the "What to Expect" books (which I HATE) said he should. His pediatricians kept saying, "Well, we'll keep an eye on him, but we're not worried yet." Which didn't stop me from worrying at all.
Today, he is 6 and in 1st grade. He reads at a 6th-grade level. He's been through all the Rick Riordan / Percy Jackson books many times over. Yesterday morning I talked with him about carrying -- as in, in multiple-digit addition, carry the 1. He preceded to add columns of numbers up until he got to the10s of billions. Never made a single mistake. However, he does have clinically low muscle tone. He is NOT an athletic kid. We make sure he's involved in plenty of physical fitness activities, but none of them competitive, so he doesn't feel shamed. You know when he first hopped on one foot? Yesterday [on Mother's Day :)]. Same day when he added numbers up to 20-billion-plus.
So, sorry to ramble on about my own kid. Your son is unique and like no other. He won't excel in every single area, but he'll keep finding areas of passion and fascination. And every time he does, he will amaze and astound you beyond all reckoning.