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When you use the dial bore gauge checking the clearance for conrods should you do this with the bearings installed and the end cap torqued to spec or no?
I don't think you need to torque the bolts to the stretch spec, just make sure they are tight, there is no force with a bore gauge that need the extra clamp loading.
You should do it as close to the installed condition as practical, but as David said, tight - 75-80% of spec' - rather than fully torqued/stretched should be OK with steel rods.
However, alloy rods can distort the material around the big end more and it may be a good idea to run them fully torqued/stretched as per intallation instructions, using the correct thread lube, etc.
If you have one, or can make one, a rod vise/clamp will help hold it while tightening. A bech vice, preferably with offset jaws, can work with soft jaws fitted to avoid damaging the rods.