First off, will ultrasonic clean the passage ways ? Seems to be to me the method of choice since it is "non-invasive" and "non-assaultive" to the crank. I'd suggest doing an internet search, look for a high end autmotive restoration business and ask them their experience. Your crankshaft is not the first shaft to be in this condition and not be saved. 20 miles from here we have a world prestigous Bugatti restoration service, if you know anything about classic Bugatti's they are some of the most valued and expensive antique cars in the world. I would suggest contacting these guys and if they cannot advise you, then ask them who can -
http://highmountainclassics.com/ In order to clear those passage ways, it may take repeated treatments of whatever the best procedure is, which i believe could be ultrasonic, until told otherwise by an experienced expert. Honestly, i cannot imagine you will have any luck removing those plugs that were used by the factory to block drilling access in order to drill these passageways at the factory. Those plugs not only were Loctited in, but they have decades of rust to make them a permanent unmoveable part. You may want to contact Mark McGrew at M3 Racing for suggestions, i would say Mark is the best CB750 expert in the USA, if not the world -
http://www.m3racing.com/ You have to have these passageways clean before you can consider saving the crank journals. All my opinion.
The main and rod bearing inserts come in four (4) factory undersizes.
The question is, can the journals be ground to "clean up" to a factory recommended undersize ? If so, no problem. Otherwise, you will have to consider finding replacement 10mm shaft or having 97's crank built up and then turned down to chosen undersize which is typical machine and engine rebuilding procedure. I have always heard from old and long time experienced engine builders isolated pitting of a journal does not matter as long as the crank can be turned to an undersize to fit the bearing shell. The pitted area acts as an oil pocket, provides additional cushion when filled with oil and does not affect serviceability of the journal or longevity of the engine. The crank is a 5 main bearing shaft, over-engineered to not fail, sothis pitting, especially on an end journal is not any appreciable concern.
Myself, i would not be concerned with what is done to repair the "10mm shaft" relative to value of the restoration. These repairs are all hidden and factory recommended, with exception to replacing the 10mm shaft with a 12mm bolt type shaft. The only concern i would have, would be the same as yours, it would be nice to save the 10mm shaft, because in the event the 10mm bolt was exposed, the correct 10mm bolt would be present. I'd suggest calling my engine builder, he is a REAL pro, he will know who can build the shaft up (if required) and he can turn the crank down. His name is Tom Wirth, his number is 608.493.4300, he is outside of Madison, Wisconsin. If you call Tom, tell him how you learned of his name. He is just finishing "buttoning up" my E2241 for 2157.
Just my 2 cents worth.