Here is my idea for the spool mounting/drive system. There is a M8 threaded rod mounted in the back board with nuts and washers, with 2 608 bearings held in place on it with lock nuts, maybe 5" apart. A 3/4" Class 200 PVC pipe slides on over the bearings. Class 200 has thinner walls than Schedule 40, and is common at Lowes and Home Depot. The ID is slightly bigger than a 608, but if you wrap a couple of layers of electrical tape around the bearings it will make a snug fit.
The big gear slides over the pipe and gets held in place by a small screw. The motor with the small gear is on the end of an arm which can be swung up to disengage the gears when you want the spool to spin freely.
The big gear has 4 holes which hold screws that stick out and engage with matching holes on the side of the spool. The printed sides of the spool are just under 6" in diameter, and press fit into 2" schedule 40 PVC pipe. That makes the spool about the same size as the Solidoodle spools. A 2" hub makes for a bit of a tight wind, but if you have a S3 you can print an 8" spool with 3" pipe for the hub.
You should be able to just slide the spool on to the winder, make sure it notches in with the screws, and be good to go. If you want to use it to wind filament at high speed, you can lift the motor off of it and crank it with your finger. Or you can make a disc with a stem on one side to chuck into a drill, and screws sticking out the other side to engage the alignment holes on the spool.
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