Changing Item Properties

Can I change a weapons damage via a script or event? And can I make the change apply to only a single weapon of that category without affecting the others or making a thousand different weapons?

Example:
Sword x 4
(I change one of them)
Sword x 3
Sword x 1 (This one has some property altered)

Also, can use the Note section to run code?

Q1: No - since items are not saved by instance, what you're asking for would require a script, and probably a fairly significant one.

Q2: Yes, but not by default. You'd need a script.

So could I have a weapon that deals a base damage plus damage based on the users stats? So a weapons Attack is  3 damage + the character holding its SPI?

Yes, you could.

Ok, but when you said 'You'd need a script.', did you mean a script in the Script Editor? Or could I just put the code into the Note section?

What I meant was that you'd need someone to write a script that would interpret the code in the note editor and substitute it for the regular damage formula. That would be a script in the Script Editor, and you'd need to find a script or script it yourself.

Provided that you have such a script, then the formula itself you could set inside the note.

All I'm saying is that it is possible to write a script which would allow the user to define the damage formula through the notebox; I do not know of any script which does so.