I just picked up a short block (minus pistons and jugs) for my S4R to replace the one in my 35k mile S4R that ate both of its rod bearings. The bottom end I picked up has less than 3k miles on it and was not from a wrecked bike. It did not come with either side cover, clutch, etc. Basically, just the case and innards (plus the primary gearset, oil pump, timing gears, and starter gear). The way it was shipped to me was sideways, clutch side down, in a large rubbermaid like tub, resting on a few thin pieces of foam. It was basically supported by the primary shaft the whole time. During the transit, the primary shaft blew through the bottom of the tub and was dragged all over wherever, filling the clutch release shaft hole with a lovely oily mess of crap. The end of the shaft is a little scratched up, but the threads are fine. The problem is, the primary shaft has noticeable end play compared to my old motor with 35k miles on it. I measured them both and the old motor has .08mm play, while the new one has 0.48mm. The service range for both shafts according to the Ducati service manual I have is .05-.25mm. The shaft still spins freely, doesn't feel like the bearings are jacked up, and shifts through all gears by hand just fine.
Split the cases or run with it?
Split them.
Damn it.
It's easier and cheaper to do it now rather than after you have swapped barrels and pistons over. The bearings will have turned into shrapnel, and rod bearings will be the least of your troubles.
Don't buy from that yahoo again.
Replace the needle bearing and seal that are in the end of that primary shaft.
Thanks everybody. I started pulling bits off last night. As soon as I find something to get the timing belt drive pulley nut off with, I'll be able to split it open.