I wouldn't use lapping paste other than to lap the bearing bores independent of the shaft bearing areas to size if required. If a crank isn't turning freely with the bearings fitted up tight albeit possibly on the tight side all lapping paste will do is wear the high spots off the bearing and shaft.
'Bedding in' should not be considered a means to cure misalignment issues
Much better to find any discrepancies and deal with any alignment issues first before bedding in. For instance if a bearing is a good running fit on it's shaft position when free but upon being tightened down has a marked tightening effect on the shaft – search for and cure that issue first until satisfied taking each bearing in turn. The shaft may be tight in the bearings but that tightness should be uniform throughout it's rotation – no tight spots in one, or more areas. It should not be so tight as to require force to drive it to 'run it in'.
Just about to do this with my marine engine build and will only use paraffin and oil to lubricate as the shaft is brought to a running fit
Tug