Mark,

1) Can't help you much here since I use a Space Explorer to manipulate the model on screen but generally the rotation center is the origin (I think). With the Space Explorer you can select any rotation point or axis, not sure how to do that with a mouse or trackball.

2) Right click on the stuck sub-assembly and select 'Component Properties'. Toward the bottom right corner of the dialog is a property named "Solve As'. That setting defaults to 'Rigid', change it to 'Flexible' so the sub-assembly will have all its freedoms of motion. Don't do this unless you really need that functionality -- it costs you resources to make an assembly 'Flexible'.

You can put things in your feature tree in folders to organize them and shorten the list. I do this often for hardware and also for related items like the elevator control system or trim system components in my Pitts model.