Proper method for determining bearing clearances?

Hmmm, this is totally contrary to what we always did at the dealership. We lubed the bolt threads with a grease (specifically for that purpose) before torquing. The reason given was that a dry bolt would drag or gall and not give you a fully torqued assembly.
BTW, what grease did you guys use at your dealership?

Torques are specific to the thread condition. Standard bolt/nut torques are for dry threads. There are some cases where the torque are spec'd for oil or other certain lubes. (ARP is a case in point.)

The real objective of bolt tightening is to reach a certain clamp load. Torque is an indirect method to reach a certain clamp load. There is a set relationship between torque and clamp load, and that relationship changes pretty drastically dry versus oiled versus plated, etc.; a certain torque with oiled threads will give somewhere in the range of 140% or higher clamp load (bolt tension) versus the same torque with dry threads.

A 3/8"-24 UNF grade 8 bolt is rated for a max torque of around 48-49 ft- lbs DRY. That torque level dry reaches the proof load and beyond that you enter the yield zone. If you oil those same threads, then put 45 ft lbs torque on it, then the clamp load will be around 45% higher, or the equivalent of 65 ft lbs of dry torque. That puts the bolt well into the yield zone...not good. It's not surprising that such bolts have failed when reused but IMHO it is not so much the re-use but the overtorquing of oily threads.

I don't know who put out that word at your dealership to grease the threads, but that is bad juju for rod bolts of this size and at this torque level. If you are greasing the threads on your SBM bolts, then IMHO it is time to worry and redo them. The rod bolts' designed clamp load is high and close to the yield zone, and so it does not take a lot of extra loading to push them past their elastic limits. If the SBM rods bolts were spec'd for oiled torquing, then the ft-lbs would be around 32 to get to the same clamp load. There ARE some specs set for oiled threads in certain applications; it is all up to the process, the clamp loads, and who specs the methods.

This all hangs with KK's info above: the factory bolts came in with specific coatings that gave a consistent and predictable relationship between torque and clamp load (bolt tension).

FWIW I have been pretty good at cleaning threads on head, main, and rod bolts forever, so I suspect that has helped me to not have failures when reusing bolts/nuts. I often use brake-kleen or paint prep on them to get them clean and dry, including the holes in the block for main and head bolts. (Dry threads are also important for Locktite to work properly on the rod nuts/bolts.) I also make sure that the faces where nut faces or bolt head ride on the caps are smooth and clean and free from burrs.