The independent moving beds seems like an over complication of a simple problem. In essence you want to increase the distance from extruder to bed, but by placing the motors closer to the top of the tubes, gearing the insides of the gear wheels keeping the same cog ratio, you should be able to reduce the overall footprint of the vertical members and mount the head gantry on the Z axis. Using three rails and one z axis threaded rod you can keep the number of parts down while keeping the simplicity of the original design in a multi-bed printer.
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