That is an interesting idea for aligning the motors. I assume you mean adjustment in the z-axis? If so, most of us have found that setting the motors to the most often used stock thickness and leaving them there is fine. I have set mine for 3/4" stock and have cut 1/8 to 1 inch stock without changing the motor mounts and without any issues. If you are planning to have a very large difference in stock thickness where the median stock thickness would be more than about 1/2" from the minimum or maximum stock thicknesses, then you might want to move the motors. But I think for most of us, constantly moving the motors is unnecessary.
As for the unistrut frames, you may want to do a quick search while you wait for the folks on this thread to get back to you. I used only one piece of unistrut for my frame (the top beam), since the rigidity of the rest of the frame is less essential than that of the top beam.
This might also be of interest to you: