Definitely want to stick with the stock size (24" or 25" depending on the year), the old hondas are slugs without slowing them down with bigger tires and you should have all the ground clearance you need with the shaft drive rear.
I would go with something on the more mild side for the rancher, Maxxis Sur-Traks are a pretty well rounded tire for the rear, they grab good in just about anything but still give you the possibility of breaking them loose and sliding it around a tight corner without flipping it over. Also pretty light for a big tire and I never had a problem with leaks even riding in a lot of rocky stuff.
I wouldn't bother trying to milk any more power out of it, pipes and filters really don't make any real difference on quads like this. There's just too many bottlenecks in the system and the exhaust and intake are really the least of the restrictions. The big restriction on these engines is the little 2 valve head, really no room for additional airflow, and the carbs are small as well for the engine size.
Other than being a little low on power they are good quads. The only problems that seem to plague them are some electrical issues related to the electronic shifting, and like all drum brakes they never seem to work quite good enough. You can beat the hell out of them all day and never bust em, all the old Hondas are that way, 99% indestructible. Probably one of the most reliable pieces of machinery ever created by mankind.
