Oh boy do I know about micromanaging. lol
It sounds to me like you are doing the right thing. To get a horse to have a mind for himself and make decisions on his own is wonderful. You are right to be supportive and available when he needs it, and to allow him his job when you can. That will make a relaxed, confident horse in my opinion.
Once he has gotten good enough where you can start adding in some stuff, that is where you can start to manage a bit more. For instance, instead of allowing him to keep taking them long or short, ask for it. Intentionally ask for a long distance, intentionally ask for a shorter distance. Ask for a trot in the middle of a line. Train him to be ridable, & adjustable. If everything is left up to him, when the time comes that you need to whoa a bit he might not hear you or know how. With green horses you leave some of it up to them to figure out, and some of it is your job to show him the way. Its your judgement call.
As far as the distances go, set up a pace and stick to it, all the way through. Pick up a nice steady canter, canter to the fence and leave him alone. See what kind of fence he takes. If he takes it long and awkward, next time lengthen his stride a little and see what you get. Try not to pickup a canter and change its pace and rhythm as you are approaching the jump, because he will have a harder time finding his rhythm and balance. Teaching him to remain steady from the get-go is very beneficial. The more times you repeat a single cross rail at a steady canter he will learn to figure it out himself. Just explore and see what type canter he does best with. Little by little you can start to help him out if you see the distance and he doesn't.
A good thought on distances is, when approaching a jump the horse sees his distance (if keyed in on the jump, some horses are oblivious) way back, sooner than you. If you change the distance right before the base of the jump you will most likely off-set your horse's balance and timing, so it is best to allow him his job, as you are doing, and remain steady and rythmical and the rest will follow.
In riding, a horse's energy is like a river- guided by the banks but not stopped by them.