Kevin,
I agree with you that it is impossible to keep stocks of things such as side rods on hand 'just in case'. That's the advantage of having another loco of the same type on hand so that parts can be 'borrowed' in an emergency while the defective one is repaired or a replacement ordered. It was common practice here to cannibalise parts like Westinghouse compressors or a dynamo off an engine that was stopped for another reason, if no spare was available. Of course, if you do that with side rods the measurements would need to be carefully checked and they might well need re-bushing.
Here too, (Queensland, Australia), locomotives occasionally ran hot bearings after overhaul. I wont say it was a common occurance but it did happen. Normal practice after a workshops overhaul was to run a "light engine" (loco without any vehicles) trial and sometimes 'break them in' with a shift or two of shunting (I think you call it switching). The latter did free up some of the stiff parts, like reversing levers, much to the agony of the men working them, but often did not involve enough continuous work to identify the likes of coupling rod bushes that were 'a bit tight'.
I remember once seeing an old driver with an engine on its first main line trip after overhaul and the right trailing coupling bush ran hot. His remedy, which would probably make some shudder, was to remove the oil cup and put a pinch of salt in the oilway replacing the cup and filling it with kerosene. He worked the engine hard over the next section and the over-heating disappeared. He then refilled the oil cup with bearing oil. I have also heard some claim that castor oil is a cure for bearings that are inclined to run hot, but I've never seen it done.
You say that you can't help but think something is out of wack and go on to mention that frame work was done at last overhaul. I presume that the measurement between the axle box centres was checked against those of the rods before the motion was re-assembled. Similarly the length of the connecting rod also has to be examined. Here, this was done by moving the engine through one revolution and comparing the movement of the crosshead with predetermined marks on the guide bars.
Mike