The older es models are senstive to voltage, and if the battery is original, Id have it load tested. Make sure the grounds, and connections arent corroded or oxidized.
Has the clutch adjustment been done lately?

 

Using the limp home lever, and having the gear flash is normal. Its telling you the es has been disabled, because the lever was used. The ES buttons wont work, until you cycle the key to off, and back on, after using the lever.
Usually doing the clutch adjustment will straighten out the newer es models, no biggie, just do the adjustment at every oil change.

 

..Hey quicksilver..Im getting 3 flashes on my 05 Racher 350ES. I'm haveing the same problem,it wont go into gear,unless I do it manually. So I am getting 3 flashes,witch one is the angle sensor,and how do I test it..Thanks again Patrick

 

ok none of the 1998 to 2001 450's you CAN NOT get codes from the ecm. Sounds like a speed sensor, but on these older ones some times easyier just to put them both in (and the angle sensor). It's really some times a guessing game, need the manual to test the compeneits. Honda told me not to go with the specs on the angle sensor if all else tests out good then to replace that.

To the guy with the Rancher, you have a angle sensor that is bad that is a code 3

 

Today I replaced the speed and angle sensors. Thing works like a champ now. Total with parts and next day air was around 200 bucks but I took it for a great ride today makeing it worth it. Thanks for the help. I saved the old angle sensor and one day when I get bored I plan to put it back on and see what happens. If it works then I have a spare.


BTW I am a happy owner of a first gen vr4

 

Other intresting part that I have learned.

Yesterday I did some pretty deep water crossings. After a bit My quad wouldnt even try to shift. Reset the key several times to no avail. I used that stupid limp home lever (does suck but did get me home) and checked it out. The angle sensor had been filled with water. It apears that there is a landing for a seal on it but neither my old one or new one had a seal of any kind. I found a perfectly sized O ring and put it on after using some air to blow out the sensor. Then I still had nothing at all. Tried other sensor and still nothign. Finaly I decided to pull the cover to the shift motor. Lots of verry nasty dark water/mud came out. I also noticed that one of the brushes was stuck to a point where it wouldnt touch the armature anymore. I took everything apart and cleaned it all with breakleen. I also took a small round file and cleaned up the brush contact surfaces. Getting this all back together was quite a trick, (the brushes are tough to keep in place while putting the armature back in place) Then I used High temp RTV to make sure the casing sealed up water tight. I found this caused the motor to bind up a bit cause I took out the old factory worthless gasket infavor of the RTV. So I took it all back apart and put small O rings behind the cover, makeing sure to get a good seal with the RTV again. Now it works perfect again and all is water tight. If you are capable of doing this I strongly suggest anyone with the ES goes and seals all this up before they regret it

 

Good post, and good find.

When I was in the market for an ATV, most of the dealers told me that any electrical problem was usually due to water damage 90% of the time.