[QUOTE=Aside form the above, all I can think of is that the alignment was previously made with the bushing already worn out, and putting a new control arm in changed the whole alignment...[/QUOTE]

That's about right.
Switching the bolts front to rear I doubt made any difference if you may have done that while installing the new control arm.

I wouldn't think you need to change both lower control arms; repair the center link then get an alignment.