That’s awesome! Do you ever experience breakthrough symptoms when starting back up?
The two times I had really bad flares that put me in the hospital and on I.V. steroids, I rested up for months as I recovered and started back exercising very slowly. If you are run-down from a bad flare, excessive exercise is a bad idea. On the other hand, if you are feeling strong and fully recovered, and it sounds like you are, then go for it.
I agree with Sara14, you are either flaring or you are not, and if you are not, just live your life to the fullest. Of course avoid antibiotics, NSAIDS and triggery foods, but exercise is good for you.
The main reason I wouldn't run if I was in a mild to moderate flare, is because I would likely feel like I was going to crap my pants the whole time, and that's no fun.