locomotive,
They go in the holes located where the bearings sit. It's now been a long while since I've been there so I can't use memory to answer but don't need it. I don't know of any manual that shows 6.
Which one are you referencing?? The manuals I'm aware of show this.
Parts Manual:
GROUP 10-03 -- CRANKSHAFT
635377 Dowel, crankshaft, bearing.......5
Confirmation from the same manual on Fig 7 -- CRANKSHAFT AND BEARINGS, show the same. From that illustration I see two on the rear and center (top and bottom bearing sets) but only one on the front bearing. The figure doesn't clearly identify which half of the bearing the dowel anchors, however I can see which side it goes in using my other manual.
Service Manual (SM-1002-R6):
FIG. 31 -- FOUR -CYLINDER L-HEAD ENGINE -- SIDE VIEW, section D, pg 29.
Para D-23. Remove Crankshaft, Para. D-31. Inspection (text covers dowels)
FIG. 72 -- SIDE SECTIONAL VIEW OF F4-134 ENGINE, section E, pg 59.
Para E-26. Remove Crankshaft, Para E-34. Inspection (text covers dowels)
These things can happen when you aren't prepared (happened to me) and you expect someone else to keep on top of everything. I've lost parts like this but I've also recovered some once I've realized what happened.
Have you gone back and asked them if these dowels turned up in their collection of junk/debris after cleaning? Being available through vendors is a good thing.