If you go to order new parts, what you're looking at are actually called "steering stem" bearings.
I looked at the parts diagram and it confirms what Gerry reported that the small ones are on top and the big ones are on the bottom. Unfortunately, Yamaha doesn't sell the individual balls, just the bearing retainer assy. that already has the balls loaded up into the cage.
New ones are about $22 for the top & bottom set, but as qwerty mentioned the AllBalls tapered roller bearing replacement parts are the way to go and can be found for about $15 more. The tapered roller set is a far more robust configuration than the OE ball bearing setup.
I've used the AllBalls steering stem bearings on several old KZ's in the past and it totally eliminated any notchiness felt in the bars and made the front end less twitchy; felt noticably more solid. When the time comes that my triple tree gets removed, I'm swapping the TW over to AllBalls whether it "needs" it or not.
When you go to reinstall your missing balls, slather grease in the bearing cup and it will keep your balls from getting away as you put it back together. The sticky lube is the key to keeping those balls where they belong.
If you have an 'old world' bicycle shop in town, you maybe able to get some new balls (set) that are close enough to work for you. I am as well using a roller bearing set on my TW/Tri-Z forks. If cash is tight, you can Pay Pal me $7.00 and I will send you my stock 06 set first class mail on Monday. Gerry