it runs better with the choke out because its jetted lean from the factory. Rejet. Your cutting out at highway speeds is likely the vaccuum line between the carb and petcock. Replace it with reinforced fuel line, replace the petcock with a yamaha raptor 660 petcock, convert the stock petcock to manual (in the tech section), or just keep running in prime.
The "shifty" 4th-5th shift is normal. Keep upward pressure on the shifter until you let the clutch lever all the way back out.

Well, at my age I like crusin at 50-55. Today I ran it up to 80, just to see if it would do it, and it did, no problem. But if it would have started crapping out at anything above 70, I don't think I would have concidered it broke !

I agree you are having vacuum actuated petcock issues -- interstate running at 75 mph used to cause me to have "false low fuel incidents" that would put me on reserve and have me headed for a gas station -- same story it stumbled like it was out of gas.

When you are running fast your vacuum level drops a lot, sometimes down to less than what will run your petcock once it gets old and flabby and the rubber diaphragm and valve seals have degraded a bit.

Solution for me was to switch to a $24 mechanical raptor petcock.  Now I have no issues at all on the super slab (except my legs get tired and start to cramp after enough of it)


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quote from tech section post

2003 yamaha raptor 660 petcock fits

Franch posting today at 02:47:14

fuelcock part #  5 Lp-24500-01-00    
$20.89 from bike bandit plus shipping. it's a direct bolt on.
comes with o-ring.
not as pretty as the original part.
no vacuum line needed.
has on, off and reserve.
must manually turn off.
the nice thing is this petcock doesn't go under the tank towards center of the bike nearly as much as OEM so taking the tank off and on won't be such a tight fit.

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At Ron Ayers Motorsports, it cost less money.

http://www.ronayers.com/browseparts.cfm?SearchString=5LP-24500-01-00&adv=5&kw...

$15.61 isn't that bad a price.

Ron will charge you $9.00 flat rate for shipping.

$24.61 to your door

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Now, Franch gets full credit for his marvelous find.  But please, somebody who does this who owns a camera please fill in all the blanks by posting appropriate additional information below.

the reinforced fuel line i suggested was intended to replace the crappy vacuum line that comes stock. If you switch to the raptor petcock you wont need a vacuum line as its gravity fed. You will need to plug the vacuum port on the carb though.