Well IMO some good full coverage aluminum skid plates is one of the first mods I do, never can tell what I will be riding over so I like to have good protection. Other than tires and a good winch are usally mine. Any thing after that all depends on what kind of riding you do box, windsheild, gas packs.
Disable the feature that restricts you from shifting unless you have the brake applied.
Disable the feature that restricts you from starting in gear unless the left handbrake leaver is depressed.
Apply dielectric grease to all wire connections that you can find, being sure to get the front diff connections and the sparkplug cap.
Those first two are freebe's now the most critical one that will cost, I have mentioned many times before on this site and that is install a Pro Design adapter in your airbox so that you and buy and use a filter that attaches to the adapter via a clamp. You can also do this modification for less money than the Pro Design adapter by finding a flanged 3" adapter at your local hardware store then installing it inside your airbox.
Then as Xtremegrizz mentioned a winch is pretty much a necessity. Hopefully you do not need it but if you ever do get in a situation where it is needed it pays off on the first use.
I just find it much more convienent to have those two "safety" features removed. There have been a few instances where being able to shift without applying the brakes have helped me keep the machine right side up. If you have other people riding or young kids playing on your machine then it is best to leave the starting with brake applied active. I found that in time it took more brake pressure to start the machine, seemd like dirt or moisture maybe gets into the switch. Myself I would disable them again right away on a new machine.
The only time I have ever tried to go into gear with the engine at a high rev is at startup with the choke still applied and it would lurch forward. If I don't want to wait until it warms up I make sure I am in gear before I start it. Not warming up isn't a good practice and generally I give a good warm up but there have been a couple of times when I didn't have paitence!
I don't mind the safety features as far as shifting and starting goes. I see the need for the reverse rev limiter as far as the manufacturer goes. I had a 01 Raptor that came stock with no reverse rev limiter. One time I backed out of the garage at about 40 mph and ended up in a ball under the deck. In 02 they put the limiter on the Raptor.
I think Yamaha actually made it so you could by-pass the limiter fairly easily.
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