Finding your cone length will be easy if you already have the lenses. You can hold the lens under the lensboard area and get an good idea of the flange focal length needed for the cone to obtain focus. Personally I think it would be much easer to use a single cone and make the focus track. If only enlarging to two sizes then only two positions on the focus track need to be specified.
Even though you may not be interested in the autofocus function, you will still need to construct a focus track to hold the wheel in position. Since you need a track, why not at least make the wheel position correct for your two common magnification sizes.
Just prop the wheel to the position to get in focus and record the distance the wheel is offset. Do this for a few points and draw it up in CAD and have someone make the focus track for you in carbon fiber or whatever.
I guess if you are handy with CAD, you could draw up concentric cones with a screw/helicoid and have a single adjustable cone. In fact the Leica autofocus enlarger had just that. Although the helicoid for the lens is to fine tune the autofocus system, it can be used to focus when projecting outside of the autofocus range (on the floor, for example).
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