This is one of those subjects, that if mentioned to a mechanic/machinist, they will look at you like you have three heads.
It's not normal practice on many engines to swap out rod bearings as preventive maintenance. Most other engines fail long before the Yamaha does, for other reasons, so it never gets to the point of rod bearings.
There's many arguments as to what makes them fail in our cars. Improper maintenance, lugging the engine, etc. Point is, we know it's an issue so we do them before they fail, to avoid having to do machine work to the crank and rods.
To educate the OP on the subject:
Rod and main bearings are made of a softer material than the crankshaft, which makes them the sacrificial piece in the puzzle. Normally, when rebuilding an engine, the machinist would measure the crank journals (where the rod and main bearings ride), look at their condition, and machine them as necessary. This may be a simple matter of polishing a few ten thousandths of an inch off and installing new bearings, or if the journals were damaged he'd have to machine the journals undersize and install oversize bearings to take up the gap. He'd also measure the rod bores to see if they're out of shape or oversized, and machine those if needed.
After all this is done, he would use a material called Plastigage upon reassembly, to check the clearances between the rod and main bearings, and the crank, and compare them to the factory specs, as a double check to his work.
All of this is expensive though, and really not worth it on our engines at this point. There's a lot of 3.0 and 3.2l engines to be had in junkyards, SHO vendors, parts cars, etc. so it's easier and cheaper to swap engines if there's substantial crank damage because of failed bearings.
Basic rule of thumb when doing rod bearings in our engines: if the journal is not scored, doesn't look worn, and you can't catch a fingernail in a scratch, it's OK to simply replace the bearings and call it a day. You can Plastigage upon reassembly if you'd like, just to see what your clearances are, but 99% of the time if a bearing hasn't already spun you'll be fine.