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The clearance between the pistons and cylinder wall was set to be pretty tight. The idea was that you could sand the wall and the piston so that it would be smooth with no layers showing so that there would be less friction or binding. You can always scale down the pistons slightly if there is still too mush material to be removed. As for the timing gears, I havent experienced much friction at all. I updated the assembly drawing to show that there are 2 jam nuts behind the bearing to help keep the gears from moving side to side. Also, I hit every gear tooth with a tiny flat file to help smooth things out. But you can also scale the gears down too if you want.
Let me know if you find any other issues.