I'm not sure I can answer all your questions without more info, including the model, as @jhackney1972 mentioned, but I can try to comment on some of them.
1. I am adjusting the opening of the vise, I have the drive link set to the vise opening value, so if it set it to 0 its all the way closed 6in gives me a 6in opening, etc. I did not realize I could drive the joint without breaking the link, thank you. (With the assembly linked, I did not have any issues with components moving)
OK, that's good, I think. If you can get away without breaking the link, that is preferable.
2. I did not use ground in the sub assembly. I joined the vise assembly to the origin when I imported it. Other than known position, is there any difference between grounding a component and making a joint to the origin?
A Rigid joint to the origin is, in some ways, better than a ground, in that, it will act to keep the sub-assembly rigid when inserted into another design. But, yes, it is functionally equivalent to ground in the design where it is applied.
3. A bit confused on this one. The joint that moved was between two components in the vise assembly. For simplicity, I have 3 components in the vise assembly, all 3 are separate components, none were created in the vise assembly: fixture plate, zero point base, vise. All of the joints for the vise jaws are in the vise. All of the joints between the three components are in the vise assembly (main part of the tree). The part which moved was the vise away from the zero point base.
Yeah, that one is hard to explain without an example. A short version is: If you apply a Rigid joint to a sub-assembly by selecting the sub-assembly from the browser, that joint will not apply to the children of the sub-assembly, which are still free to move. Let's ignore that, unless we find out it is the source of your problems.
Ill add a 4th question here, to which I suspect the answer is no. Can I adjust the hierarchy of, or move the tree location of, the slider joints so they are not buried so far down in the tree? I tried redefining the joint when the full assembly was selected, not just the vise component, but it still put the joint in "main" joint folder.
Your suspicion is correct. You cannot move a joint's ownership.
Jeff Strater
Engineering Director