How would you deal with the piston/rod assemblies?
Attempt to leave them in?
Remove them, and if so, ridge ream, hone and rering?
Assuming all dimensions justified just a hone and rering.
Any added commentary you likely have would be great to see.
I'll give you the Cliff Notes version as I have not done this on a 919 motor ... yet.
-- Once the motor has had all fluids drained and all the ancillary parts removed (exhaust, throttle bodies, chain, and all electrical connectors disconnected) pull the oil pan and clean it out thoroughly, then reinstall with four bolts.
-- Remove the engine and place it upright on a solid work surface. Remove the spark plugs and stuff rags in the open holes. Loosen all upper case bolts in a crisscross pattern and remove, clean, and bag and tag for reassembly. Look for copper sealing washers and note their location.
-- Remove the alternator, clutch, timing covers, and the alternator rotor. Remove the crankshaft right side bolt retaining the sensor wheel and cam drive sprocket. Remove the sensor wheel. The sprocket will be removed later.
-- Turn the motor over to expose the rest of the case bolts. Remove the oil pan: there are several case bolts exposed. Break loose all the case bolts in a crisscross pattern, then remove them. My preference is to tie the transmission shafts to the lower case to maintain the connection to the oil pump / water pump driveshaft. Saves time by obviating the necessity of removing the clutch assembly. You're ready to split the cases.
-- Since the cases have been together for a very long time and will be reluctant to separate go slow and find jacking points in preference to using a hammer! Once it's broken loose remove the lower case.
-- Once the crankshaft is exposed turn it until all rod caps are accessible. Break all rod cap nuts loose but do not remove them at this time. Rotate the crank until cylinders 2 and 3 are at bottom dead center, then remove the nuts on those rods and caps/bearings. CAREFULLY MARK THE CAPS AND NUTS FOR REINSTALLATION ON THEIR RESPECTIVE RODS! Slip eight inch long pieces of rubber hose over the exposed rod studs to protect the crank and bores, then turn the crank 180 degrees to access the caps for 1 and 4. The two you have already done will be pushed down in their bores. Repeat the cap removal for the rods.
-- Retract the cam chain tensioner plunger, then remove the tensioner. Clean all oil from the sprocket and camchain and make a reference mark on both for reassembly. Rotate the crank until both runs of the chain are loose -- there will probably be enough slack in the chain to allow removal of the sprocket. Make sure to tie the chain to the case to prevent it disappearing into the chain case, and hopefully keep the chain tensioned to maintain the timing of the cam sprockets. If the timing chain slips a tooth on either sprocket, trust me you will hear it, the cam cover will have to be removed to retime the cams. Remove the crankshaft.
-- From here it is a matter of sizing the main bearing shells to give the proper oil clearance by using the codes stamped on the engine case, the replacement crankshaft, and connecting rods. Once the new main bearing shells are oiled an installed in both cases drop in the crank and place a length of Plastigage on each main journal and install the lower case and torque to specification. Recommended clearance is 0.0007 to 0.0014 inch (0.017 to 0.035 mm), with a maximum clearance is 0.002 inch (0.05mm). Shoot for the middle of the range. Usually there is little necessity for redoing the bearing clearance, but you never know. Always check!
--Next, the rods. With the crank out oil and place the new bearing shells on the rods / caps, carefully place the crank, then install the caps on rods 1 and 4 and cinch down the nuts. Starting with the #2 and #3 rods place the plastigage on the journals, and install the rod caps. Once you have the clearance right clean off the journals of any gauge strip, oil everything, and install and torque the caps.
At this time loop the camchain over the crank stub and install the crank sprocket, matching the marks you made during disassembly. Install the tensioner but do not release the plunger. Rotate the crank 180 degrees, remove the caps on #1 and #4, and repeat the clearance check. Once the clearances are right put the motor back together.
Use Honda Bond only to seal the cases, and everything else for that matter. it is the best sealant I have ever used by far. Pricey, but definitely worth it.
I learned this from a Honda Racing tech, and have used it many times, once the night before a six hour endurance race when the oil pump bypass stuck open and scored several main bearings, thankfully without spinning them. Starting when we got a new crank from a salvage and assurance from the shop owner sponsoring us that he had all the parts we would need I dived in around 11 PM and had it ready to go back in the frame by 2:30 AM. We put the bike back together and fired it up. Having not slept for 48 hours, and with only an hour left before the start of the race I suited up in time for the usual "testing it out after a major problem the day before" practice, shook it out thoroughly, and did my usual Zen routine to get ready for the race. It went the distance with me doing ~70% of the riding, and we finished second in our class and fourth overall. Not bad at all.
Slept for the next 20 hours. Needed to.