That tractor looks like it has the big battery door and key start which would make it a 57 model. Now first question: Have you had it on a dyno? I have seen some of them smoke like that and they didn't have 30 Horsepower? Remember that is a diesel with a hardened crank. If you go to stoke it you will need to find someone who can reharden the crank. Also remember it has a Lanova head. That is why the recessed exhaust valves. Remember a Lanova head is slow burn. What RPM can you run? How about a Case pump with an internal spring governor so you have a better chance  of adjusting torque build-up.  Early Super 88 heads did have larger valves if you can still find one. As far as for milling the head, just get you intake valve recession set and then set the exhaust valve stem height to match. Oh by the way if you take the head off and find a dozen cracks don't get real excited!