Certainly doesn’t sound like a quartering problem as your chassis seems nice and free-running.
Fortunately it is often the way with model engineering that further consideration of a perceived problem shows that it is not as disasterous as first thought.
By your step-by step approach you should be able to isolate the point of resistance.
In my limited experience a firm grip is needed to turn a new engine over until it is run in on air.
It sounds as if you have the problem under control – (do you have clearance between the cylinder ends and pistons at full stroke?).
(It seems that only you and I have issues of this type!)