Your lens stage and the film stage isn't parallel to each other. I tried the exact method you are talking about, using Besler's alignment jib to align my Omega D2. It is possible but not terribly accurate or quick.
Baseboard being off by a few mm makes no difference in sharpness but film/lens stage makes awfully big difference even if it's off by a fraction of mm. Difficulty in doing all this is, as you said, the baseboard will have to be the common reference point. As you push UP the besler tool to the lens stage, and as you try to move the film stage, their relationship to the baseboard changes.
This is a business, correct? If so, can you hire someone who has the proper tools and have done this number of times? Or do you really want to do this on your own?
My solution was to invest in a laser alignment tool. It fixes none of the above mentioned problems but as I can see the changes in real-time, it makes the process much easier.