Usually if the caps haven't been referenced to it's rod, you can work out which goes with which.
Remove the bearing shells and then fit each cap in turn to each rod, fit the bolts and tighten them up. IF at ANY point while doing this part, of this exersize a Cap or bolt is too tight to fit by hand, don't force it, as it's likely they are not matched.
After tightening them up, visually check the alignment of the tunnel and also the thrust faces for alignment. The thrust faces though, are occasionally off from the factory but they'll only be out a thou or maybe two. If the Tunnel looks right, usually a torch from the back helps here, run a 1 thou feeler strip on edge over the parting line. If may hang up slightly on them, but will usually glide right over them. You need to check, where possible, every cap, on every rod, even if you think you have the right match.
If there's any doubt on any of them, then best off having them closed and honed, but be sure to mark them prior to doing this.