Use "Pack and Go". You can change the file names before you save everything. It updates the references. You still have to do them one at a time but all the files are listed in the dialog box.
I put a circular center mark on the hole pattern, this puts in a center line circle to represent the bolt circle. Then I dimension the resulting bolt circle. The only thing is that this dimension comes in as a radius, you have to go into its properties and change it to a diameter dimension.
I just started playing around with the "peg in hole" smart mate. It seems that this doesn't work if there are radiuses or chamfers on both ends of the pin. These features must be suppressed in order for the smart mate process to work. They can then be resolved and everything is fine. THis seems...