You should be able to do most of the construction without putting the other scope out of action. I guess it depends on how many parts you are using from the old one.
I normally only install the optics just days before first light.
The only disadvantage of not clamping the poles to the side bearings is that you increase the flexing length of the poles a bit and you have to make a structurally stronger mirror box to fasten the bearings to, as you have said.
Reducing the size of the rocker box by using large altitude bearings would help in transport (unless the other components stacked in it are higher anyway).
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