Don't over think it.
You have about 32000 spell ids you can use.
With a few queries you can pop out a 100 custom rune spells in a few seconds.
Also if you want to get a little creative. Look at spell effect id 413, it has the ability to focus rune amount values. So if you use that and set a limit to rune spells on it. You could in theory add as an equipment focus effect a scaling rune focus. So if you made like 20 custom rune spells, then also had like 20 custom rune focus spells you might be able to keep up with content scaling easier if you get what I mean.
http://wiki.eqemulator.org/p?SpellEffects&frm=Main