I was trying to figure out how to go about upgrading this weapon. I understand that it is a specific weapon that can be created. But how would one go about upgrading the weapon when the time is right.
I am under the impression that it would qualify as a +4 (+2 and wounding) weapon for the purpose of upgrading. So applying a new enchantment such as agile on to the rapier of puncturing would be 18k right?
If anyone can give me some clarification on this I would appreciate it!
As I understand it, a specific named magic weapon or armour cannot be upgraded. Certainly it's not Pathfinder Society legal, see the second point under Wealth and Treasure here: Pathfinder Society FAQ
That said, assuming that this is a home game and not a PFS game, you can always ask your GM if he's willing to home rule allowing you to upgrade the item. The reason that specific weapons/armour normally can't be upgraded is that they often have some kind of additional ability that isn't easily classified by the standard magical abilities listed under item creation, so it's really just a matter of asking your GM what total enhancement bonus they think the weapon would be equivalent to, then doing the math from there.
I hope this helps.