Crackie, if I discovered those gears in a box I was rebuilding, I would be concerned about the striations on the inner walls of the dimpled bronze bushings and the fact that the oil passages on the bushes were no longer aligned with the oil passages on the gears. Clearly a sign that at some point those gears seized up on the shaft, probably due to a lack of adequate lubricant.
I would press those bushes out and replace them, and use Loctite when installing the new ones. Even if you are successful in re-aligning the oil passages of the current bushings (whether by removing and rotating them or just rotating them somehow) or if you leave them where they are and just cut a second set of notches where the gear oil passages are, you will still have those rough scratches or striations on the old bushes that really need to be dressed out, and that minor dressing will certainly increase the ID of the bore.
You have gone this far, you might as well rebuild it right and make sure you won't have to pull the gearbox again in a few years.
'88 Quad - "Claudia"