Rooster,
I took the heat shield off the left side that covers the exhaust manifold to see if I could hear where the rattle was coming from. It sound like it comes from what I think is the transmission( the metal casing that sits below the exhaust). I haven't got the shop manual yet. The dealer that I bought it from told me they don't sell them yet. After a few runs up and down the yard, the noise disappeared. It seemed the noisiest when it was cold and I let off the gas to slow down. Maybe it takes a couple of minutes for the oil to fully lubricate the tranny. Also, I only have about 5 hours on it.

 

I bought my shop manual from www.helminc.com or you can call 888-292-5393 (tell them it is an ATV up front or they will think it may be a car or cycle)$40.00. It is very detailed.

 

Guys,i had the very same noise with my Y2K Rancher ES 4x4 and it turned out to be a loose swingarm spanner nut.A good Honda mechanic found and corrected the problem.You need a special spanner socket and it needs to be torqued to the correct foot pound.Remove the plastic cover on the right side of the swingarm and you will see it.

 

Also purchased my manual for my Rancher from Helm. I will get one for the Recon once they are back in stock. The money is WELL worth it. $40 for the manual +$4 for shipping. NOt bad

 

Thanks to everyone who replied to this post, I have not been back here for a few days and I was rather overwhelmed by the response. I have bee helping relatives with their Corn harvest the last couple of days after work.
I'm still a little frustrated by the situation but hopefully after a good ride Sunday I will get my confidence back. Thanks to everyone.

 

I KNOW the feeling... I took a Yamaha in for oil smoke on start-up..
The put a new head on it, but stuck all the old components in the new head WITHOUT rebuilding them.. (4 weeks) I went to pick it up and it wouldn't start. (another 1 week) Got it home, rode it five minutes and it was rattling so bad I shut it off and PUSHED it back down the driveway. Back to the dealership, ANOTHER top end and a set of rings (another 5-6 weeks) Went to pick it up, started it up.. RATTLING... was told, "It'll break in and quit rattling!!".. (I KNEW better but hey, it was under warranty... I like the sound of engines grenading anyway) Took it riding, and within two hours of riding, it was popping, backfiring, wouldn't hardly run 20 MPH, kept dying, then started smoking AGAIN!. hehehe..
TOOK IT BACK.. they said it just needed a valve adjustment..., So, after they adjusted the valves and it still kept smoking..(go figure) I finally chimed in and asked if they thought it MIGHT need a leakdown guage put on it to find out exactly WHAT was going wrong.... THE YAMAHA CERTIFIED TECHNICIANS didn't have a CLUE what I was talking about...
They ended up replacing the exhaust valve and guide again... and putting ANOTHER set of standard bore rings in it..( it REALLY needed bored) and I took it to the Karnack Mudrun... Good thing I took my Scrambler as my backup.. the Yamaha lasted 20 minutes off the trailer... It started rattling and smoking... I got way passed pissed off and drove it until it blew apart...
Took it to ANOTHER dealership and let them TOTALLY rebuild/replace everything.. Then sold that POS to my brother.. hehehe...
Dealerships need to hire TECHNICIANS.. NOT PARTS CHANGERS....

 

Personally I would change the filter also. It should have a few metal shavings in it from the new motor break in. Nasty things to leave lying around if you can avoid it.

 

I would have to question how much patience there is with those who must rush out to buy anything that takes on a new design. The truly patient ones are those who wait a year or two for the product to prove it's reliability.

 

I didn't see where anyone posted the reset procedure for the Ruby...Mine has worked great for the first 300 miles but I was just wondering what to do if I have problems on top of Black Bear Pass in Colorado.(almost 13000ft.) Will disconecting the battery work?

 

I got this from another post in here. I have not tried it though since mine works fine.

Rubicon reboot procedure

1.Start the engine and let it idle about one minute with the sub-transmission in neutral. Stop the engine.
2.Make sure that the gear shift is in the neutral postion (be sure the neutral indicator comes on) and turn the iginitins switch off.
3.Turn the ignition switch ON while pushing the UP and DOWN shift swtiches (ESP shift switch) simultaneously.
4.Release both the UP and DOWN switches immediately, then push and release the shift switchs in the order of UP, DOWN and UP (Do not hold onto the switch).
5.A constant "--" indication stays ON on the gear position indicator. (If the gear position indicator shows the continuous lighting of "N", repeat the procedure from step 2).
6.Move the throttle to the fully closed position, then to the fully open position, and then to the fully closed position again immediately (within 10 seconds) after "--" comes ON on the gear indictator.
7.Check the control motor operation sound (the control motor should function at this time to adjust the angle sensor).
8.When the initial setting procedure is complete, the indication on the gear position indicator changes from a continuous lighting of "--" to the continuous lighting of "N".