Just wondering if the pilot jet actually has a small hole all the way through the centre to which you can see light pass through.The side holes are all clear but looking through from the end of the jet with the screwdriver slot I see the hole but no light passes through.I'm using a spraygun cleaning probe kit and can't get them to pass right through the jet.The bike runs great and pulls hard but won't idle unless I leave on the choke all the time.Any thoughts would be greatly appreciated.Sorry for the long and drawn out question! trying to be overly descriptive.

What you're describing sounds like a plugged jet.  There is a tiny hole straight through.  Your probes are likely too large.

I have used these brushes and cleaning needles to clean pilot jets and starter jets, the cleaning needle sets can usually be purchased at your local welding supply store as they are used to clean cutting torch tips.

Pilot jets have a pretty small hole through them , and are one of the easiest to clog up .
Why not just replace it outright with a new Yamaha or Mikuni jet .

I have welding tip torch and paint gun cleaners and none have a wire small enough to fit in the tiny pilot jet hole.  

Ultrasonic cleaner or a strand of copper wire is what I've done...  I don't recommend poking things in jets though. 

I agree with Swoop, if it's that bad might just as well replace it.

Monofilament fishing line of various weights can be used as a safe poker for small jets.

The welding torch tip kit works fine for the main and pilot jet, and then I follow it up with the brushes. I do as MarkT suggested on the starter jet and use a strand of copper wire to clean it out. I think we need to give people some credit on their intelligence level, I hope no one is trying to ram something through a brass jet, yes you can damage them, but I seriously doubt any one would feel a noticeable difference in performance, usually a chemical soak for 24 hours and you can blow through them with some compressed air, just don’t do like I did and blew the jet out from my grasp deep into the black hole corner of my shop never to be seen again. Again as swoop suggested they are cheap enough and readily available to buy new, maybe it’s just me and I don’t like to pay $7-9 dollars on shipping for a $4 part that can fit in a first class envelope. 

Got a wire brush ? cut a single strand off and that will work in a pinch,
or
www.mfgsupply.com/snowmobile/snowcarb/sn...ilotjets/07-545.html

Just had to find the right probe.Spraygun cleaning probes go pretty small.The jet was really plugged bad but after continuous carb spray and working in the probe it finally cleared and voila!! "Light at the end of the tunnel". Bike idles perfect now.Thanks for all responses. 

I just pull a strand out of my wire brush--its looking pretty bald these days as can never find the old strand next time i need it. Not a big hole so have to line it up good to see light through it. But yes what you're describing--choke on to make it idle--is likely blocked.
Reminds me i saved a bunch of acupuncture needles once after getting prodded & poked. They worked well but smaller than required but would dislodge the blockage if its not clinging to the sides grown in there.