I had a similar problem.  I "solved" it by using a toothed timing belt 
between each screw, such that both sides were forced to stay in 
alignment.  That way, I didn't need to worry about misalignment during 
either homing or actual milling.  I only used one homing switch for the 
axis this way.

It seems to work fine.  If anyone sees a problem with this solution, I'd 
like to know about it so I can take preventive measures.  I recently 
finished my machine, so I don't have a lot of experience with it yet.  
But, so far, it's working fine!

Dennis

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