My and my buddy are both currently tearing down our RT3s to the frame. Mine due to PO's very bad spray paint and his because of rust. When we got to the triple trees we noticed his ball bearing were all the same size and mine were smaller on the top and bigger on the bottom. Just curious about which one is right. The one with all the same was a little harder to steer but that bike is also in rougher shape. 

Parts lists have the answer...

3/16" top

1/4" bottom

You can save $ by buying them from a bicycle supply, Amazon, good hardware store, or bearing shop...

Also pay attention to race location if you are replacing them... some of the Yamaha parts diagrams have the locations mixed up.

As MarkT says. & has 22 top & 19 bottom--without looking. Don't go one more [of the correct sizes] or you'll have problems as not enough room although you might get them in but will bind up on adjusting.

I heard of people replacing the loose bearings with tapered bearings and races to match. Anyone done this and is it worth the trouble? 

I have All Balls tapered bearings and races in two of my Yamahas. I think the original balls are just as good. I don't ride any of my bikes like they should be ridden, so maybe if I rode them as intended the tapered bearings might prove to be an advantage, but I am skeptical that that are any better.

Thank you! I did look for the answer but came up with nothing.. I have heard of replacing them with tapered bearings but sounds like a little more work than what its worth to me. 

Also, my raceways appear to be in good condition. Is it something you should replace while you're in there or if it looks good its good? First time messing with the steering.

If they look good, I would clean them up and leave them alone. In my opinion they are not hard to replace, but if its not broke don't fix it. When I first started rebuilding my bikes I was obsessed with somehow making them better, but that obsession is gone. I just want to get them rideable.

On a lot of Yamahas of this era, the aftermarket upper tapered roller bearing/race sits too high. Some have compromised by going for an aftermarket lower tapered bearing, but sticking with the standard upper.

+1 on MarkT's comments on sourcing the ball bearings and, if you do need them, original races are probably still available from Yamaha.

Absolutely right
on the upper tapered bearing sitting too high. That was the case with my 73 MX360.