"All conditions being equal, would a 993 engine bring much more value than a 964 engine? ie is a 993 motor worth the extra $2k."
I don't think so. The 993 engine puts out more hp because its exhaust design is better. This is a non-issue with a swap. Varioram can be a bonus, but not all 993's had it. Check
this link for the differences between the different 3.6's, as they pertain to a swap.