Welcome to ModelEngineMaker !If you have problems registering or logging in, please use the contact menu option to request assistance.
With the ends screwed onto the rods, you would be very lucky if they were the same length. Really they could do with a simple jig. Drill and ream one end of each, then locate them on a fixed pin to make the holes at other end. However it is no big deal to open the holes to give a bit of leeway. Locomotive coupling rods have to have a bit of clearance to allow for uneveness of the road.
You could keep the same basic rod design, even one end could be screwed on and held with Loctite so it did not turn. Make the other end a push fit so it can be slid into place and again retained with Loctite as there is no thread you will not be spacing the ends to the nearest half a thread pitch.Or you could just unscrew one end and turn down the male threaded end of the rod . make that the push fit end but use an epoxy like Araldite rather than Loctite so it fills the thread in the existing rod end.Ideally when you assemble make a simple jig - just two pins sticking out of a piece of flat bar which will hold the two ends to a set distance while teh Loctite sets on the unthreaded end.
Clamp the two pices of flat bar together and drill through both then the hole ctrs can't be different.
Looks like you have the two rods/pins 180 degrees apart? If you make them 90 degrees apart, then they will not oscillate. Just like a two cylinder crankshaft - one is going past top/bottom center while the other is in the middle of the stroke. I'm assuming the two valve cranks are connected to a common shaft through the valve?
Boy, looking at the video the pins sure look 180 out from each other, end to end on the same shaft. Hard to tell without a side/end view though! Another thing that HAS to be the same is the distance from the center of each disc out to the center of each pin, on all four pins.