Any Codes flashing on the display?
Because I'm not familiar with what accessories your Rancher has? Do you have a Tach? If so at top speed what does the Tach indicate?
There is a possibility even though the engine sounds good, it may not be getting up to full RPM? Plus you're suffering Power loss you aren't hearing yet (you may hear a pinging sound? at full throttle at top speed). I'm thinking because you haven't ridden it much (154 miles since 04?) the problem is in the Carb. Fuel does some nasty stuff when it sits inside of any Carb for any length of time. Because the fuel has been sitting idle (no pun intended) for so long, it does break down and looses much if not all of it's octane.
I would change out the fuel, and remember the newer blended fuels start to break down much earlier than the stuff you have in the system now (usually within 6 months for the new stuff) And I would also add a fuel system cleaner to the new fuel you put into your tank.
I know there are quite a few other fuel system cleaners on the market that really do well. But I have used Chevron Techron (in a black bottle, and more expensive than most) with great success. I would do this all right before I took the ATV out for a good long run. It's my belief that between the loss of octane and the fuel breaking down, you're loosing top end RPM's and Power.
I would do this before spending money on anything else. Also because you don't run the engine much. I would install a fuel shut off (if there isn't already one in the fuel line?) and when you finish using the Honda, I would turn the fuel supply off while the engine is still running. Once the engine quits, turn the ignition off. Now the fuel if it goes bad again won't crud up the inside of the Carb on you.
Good Luck (Bustamove)