Assume your are also upgrading the inner cam bearings as well but, if not, consider incorporating that upgrade in the project. The rear wheel only has to clear the floor; not sure why jacking up the bike is a problem. If using a scissor jack located under the frame cross member the bike will be stable; I have had one of my bikes sit in that position, on a lift, for days. If worried about stability, just get a ratcheting tie down and snug the bike to the scissor jack; it won't be going anywhere.
The oil pump alignment is simply centering the pump on the pinion shaft and aligning the gerotor flats to the pinion flats. It doesn't require much rotation to accomplish that. I forgot to include using the alignment pins to assist in the oil pump alignment. The pins will center the pump on the pinion shaft but, IMHO, may not align the gerotor flats to the pinion flat, so, again, JMHO, a bit of rear wheel rotation is still required. Being a "belt and suspenders" type, I use both the pins and rotation. If the only rotation required was for the purpose of pump alignment, rotating from the pinion side (plugs out and trans in neutral would probably not present any problems; your call. However, even if you have retained the OEM pushrods, you will also need to rotate the rear wheel to set pistons at TDC to re-install the push rods and rocker support plate. All the more reason to avoid rotating from the pinion side IMHO.
A couple of suggestions for your consideration. Get the alignment pins from Georges Garage as well as a remote start button that connects to the starter. Plugs out, trans in top gear (5th or 6th), use the remote start button to turn the motor over when necessary to complete the project.