It is always better to prepare carefully than to regret what you did later. When I made the R8 conversion for the museum's light vertical, I spent ten times as much time setting everything up to be perfect and better than my normal work. There was no second chance to get things exactly right and to my great relief, the results were even better than expected.
You could move the work between cuts, if the length of cut is too long. Careful re aligning should work fine.
When we had only the drill mill at the museum, I found that the slot in the bed which was used by the vice keys was not very good when the vices were used as a pair spaced out. The X movement is 500mm, and the bed is about 120mm longer, so getting the slot running true to the ways was not easy. The head had to be swung at about 40 degrees either way to mill the entire edge of the slot. Now the slot is within 0.001" of true which is an improvement on the 0.007" before. Before any cutting, the entire length was mapped and because the worst error was positive, most of the cutting was only 0.001" deep to clean up.