what i'd do [not always right lol] is build it up to a 'rod' side clearance incase of slight variations with say an aftermarket rod kit or thickness of washers. I just slide a feeler blade in & press [tap tap tap under press pressure when near the mark]. Then--ummm, [been a while] measure across the webs where the bearings but up & then somehow measure between bearings in the case with cases clamped together then calculate the difference [another then--] decide if you need to space it over from the primary side only to get rod in the middle as it's held tightly towards that side by the crank nut--then--now i'm confused but that's the guts of it. Good luck. ps, i wouldn't blame your mate [unless an obvious mistake] as i'm sure he did his best and possibly other [unknown forces] things came into play--was it new bits or 'best of the rest' etc. Hope the rebuild goes to plan. Cheers.