Drilling/reaming the hole in the horizontal CI bearing is where the trouble is.... most likely the hole did not drill perfectly straight. Small drills will walk off center very easily. Just drilling/reaming typically won't cut it. Measure the wall thickness all the way around the bearing on the far side where the drill exists and I'm betting you'll find it's off center from the small drill wandering. I played with ways of getting this hole concentric by using a drill chuck in my compound tool holder vs my tail stock and had some success, but the easiest/best way I found was to turn the OD oversize and drill the hole. Mount the bearing on a piece of whatever you are using for the rod and super glue it so it's secure. Mount it up in a collet and then turn the OD to final size. There's more than one way to skin a cat! But trust me this hole must be perfectly concentric.
I followed the design materials to the letter. Brass cylinder and piston, brass displacer, CI bearing for displacer rod, etc.. All that is good. One possibility with your model is the weight of the displacer... I made mine very thin with ~0.015" walls from a solid piece of 360 brass. You need to keep the weight as minimal as possible to help with the cantilever binding in this design. If your glass displacer is heavier this will cause additional issues. I know of one guy who ended up making his out of aluminum to minimize weight and it seemed to help. You can make them out of free machining brass very thin, but you need to sneak up on things very carefully. I've posted how I did mine so maybe if you do some searching on this group and HM site you'll find my multiple posts on this subject where I made mine and helped others.
Not sure why you have the screw adjustment on one of your linkages.... All my parts were made to spec so you might want to check that your linkage is set at the proper length for the proper stroke...
Also, don't be afraid of putting a drop of oil in the horizontal CI bearing, especially when first trying to get it running. I would NOT oil the power cylinder as burnt oil soot will build up and then the engine will stop running until cleaned. Keep the oil out of the hot running components.
Ted