You do need an alignment tool to do the job correctly. Changing one at a time means nothing in your case as you are getting new mounts. They will not be exactly like your mounts. A 1/16th inch on a mount means a pretty big difference back at the pump.
It will put a side load on the pump, engine PTO, and wear ring..
Here is a link where I rent an alignment tool, in post #1 I added a video of how to use the tool and align the motor.