Shouldn't be a problem at all to replace the internal parts of the valves. You probably won't need to dig around the valves unless you feel you don't have enough room to work in the valve boxes. As far as the Hunter valves go, I believe most of them have 4 screws and the top just tops right off (you need to unscrew the solenoid first), unless they are jar-top valves, which I doubt because the jar-top valves are a newer feature. Simple as switching out the parts once the top cover is popped off. There should be no gluing involved, and you shouldn't have to re-connect anything to the mainline (or waterpipe). As for your problem with Zone 1 and 2, it could fix it, but there might be other underlying problems as well.
Tony Posey
Ridge Run Landscapes