Hope I'm not too late to the party... Did you ever get an answer to the sizing?

Wow, I can't believe the manual doesn't cover what size the bearing colors are... How would we ever be able to know which ones to order lol. Looking around on older forum posts for lots of other Yamaha's, this sounds like a common road block.

You can verify the order of the bearing colors with a micrometer that has a ball on one end by comparing the bearings you have in hand. Although they're worn, you should see a pattern that the three greens are similar in size, the yellow is the larger, and brown being the smaller. Their difference in thickness should give you a close idea as to the step in sizing for each color especially if brown-green jump is similar to green-yellow. In my most recent experience with GSX-R motors, each bearing color is approximately .004mm different from the next color. Point being, the steps are usually pretty small. If the step sizing is similar to the GSX-R, you may benefit from going down 1-2 sizes where you read .051mm. You may already know this but in case you are not aware, you're also safe to extrapolate to the halfway point with the plastigage. If your gage thickness is right in the middle between .038mm and .051mm, you can safely call that .0445mm (rounding). Were your .051mm plastigage measurements dead on the .051 mark or were you rounding up or down? Plastigage is very accurate but unfortunately not very precise. In other words, if your reading is in the range between .025mm and .038mm, then it's definitely in that range but where...

I have great success measuring my theoretical clearances based off of unassembled dimensions (e.g. measure the crankcase journal surfaces when mated, subtract the crankshaft diameter for that particular journal, then subtract the two thickness measurements for the journal bearing halves, you should be left with your oil clearance), then comparing these calculations to my plastigage readings. There is usually a discrepancy but it's usually consistently biased across all my calculations. Because the plastigage is a measurement when actually assembled, I tend to lean toward that as my final clearance.

Lastly, I always* torque all bolts, even just for oil clearances. This helps ensure the cases sit as square and tight as they will when it's running. *Some manuals specify only the main journal bolts need torqued. In that case I will do as the manual bids.

 

Thanks @terrusamoto !
I've got the engine back together and back on the bike. I just went with the bearings I had which were new replacements of the factory spec. J2-J5 plastigage most closely matched the .051mm bar but it was close. I figured, like your good recommendation, if it's slightly in between, that puts it in .045mm realm and in spec. Also figured better .006mm loose than tight. Talking to engine builders and drag racers. Tight makes heat. Loose makes power.
Engine is purring beautifully! But I must have assembled the transmission wrong as its making some weird sounds. Gotta take it back apart...