a couple of things are going on, here, I think.
- understanding the difference between Body and Component, and how they handle Move
- understanding that sketch origin (the red and green lines when editing a sketch) is not necessarily the same as component origin. Often, they are related, but not always
- understanding the timeline, and that, when editing a sketch, Fusion "rolls back" to the point in time when that sketch was created. So, putting a Move (whether component or body) into the timeline after the sketch will not affect the position of components when editing that sketch (because those moves or Captures) have been rolled back.
There is definitely a misalignment in components in your design, at the state it was shared. The Joint Shaft subassembly is off by a bit, compared to other components (particular the global origin, and the Shaft origin)

However, that misalignment was created in the last 4 features in the timeline:

if I move the timeline marker before those 4 features, the misalignment goes away, and everything aligns nicely:

I suspect that those 3 captures and the 1 Move Body was trying to realign things, and actually made things worse.
In general, there are not usually a lot of good reasons to have Moves or Capture Position features in your timeline. There are some, particular position-based modeling, but sometimes people will try to use Move as a substitute for create component joints to connect components, and that can lead to misalignment problems. Don't want to get too preachy about it - you are free to construct your models however you want, so that is more a recommendation than anything.
And, the point above about rollback during sketch edit is important. If you want to change the position of something that is referenced in a sketch, you will need to roll back before that sketch and insert a Move or Capture before the sketch to have it appear correctly when the sketch is edited.
Hope that provided some useful information, at least, even if it did not solve all your problems.
Jeff Strater
Engineering Director