Hey Mc,
A lot of good info here for you to digest. There are multiple ways to do this as you have seen. Using the rods on your crank is not wrong, it's one of the options you have. Just depends on what you are working with. Just be sure to plastigage the bearings no matter which method you use! Since you have decided to do it this way I would suggest trying to read the rod journal size markings on your crank. This is difficult to do at best but it will help to get an initial match for the bearings provided you want to use new bearings. The lettering/numbers is scribbled/scratched on and it looks like English letters with a Japaneses accent. VERY faint usually. I just did this with my crank & rods but haven't proceeded with the actual sizing yet. My crank had J-)L- AAAAA P)L-4444. The first set J-)- AAAAA refers to the crank journal sizing and the second set P)L- 4444 refers to the rod journals. Again very difficult to ascertain. The L tells you to start on the left end of the crank to match the letters to the corresponding journal. I then took the numbers and matched them to the number I spoke of previously on the side of the rod big end. IE 4 & 2 (on my rod big end) is a "green bearing" or Honda part number 13217-300-13. This corresponds to a particular clearance. I would then get a set of green bearings for this journal and whatever matches for the other journals, insert plastigage, torque it down properly, undo it, then "read" the plastigauge to determine if the bearings fall within correct tolerances. You'd be really lucky if the new rods had the same bearing clearance designations as your old rods. If this were the case I'd probably start with the old bearings, insert plastigage, torque it all down then read the plastigage rather than order a whole new set of bearings that might need to be changed to another size, reorder more and have that much more expense for a second set. Read the plastigage and order bearings according to the clearances you get. You'll be a pro in no time. No matter which way you finally choose to use it's important to do this the right way if you want your engine to last.
Jerry