That proposed solution might be a bit more difficult than you realize -- however one thing i could do fairly easily is let the user right click and add selected clips to the stack, with CHS maintaining an explicit list of stack clips.
So that at any time you could go and select some clips and add them to the "explicit" stack list, in normal or reverse order, to top or bottom.
If i made this "stack" list visible in the options (or a separate dialog), i might even just let you edit it like a text field, so that it could specify a list of clip id#s, OR raw text.
In essence what I imagine is that the stack would work as it does now, except when you EXPLICITLY add stuff to the EXPLICIT stack, at which point those would pop off until that list was empty.
So if you had 5 clips scattered throughout your database that you wanted to pop off one at a time, youd just go highlight those 5 and right-click and say "add to explicit paste stack"; you would then be asked whether to add them to start or end of stack and in what order.
You could repeat this process to add more clips to the explicit stack.
When pasting from the stack it would proceed through those you just added, going in the order you arranged in the explicit stack.