If you add a ability to a unit with triggers, you can't upgrade them anymore.
The only solution is to create an upgrade for every spell with "Data" = "Ability Level Increasement", "Basic" = "1", "Increaseme0nt" = "0".
Also you have to add every upgrade to the "Used Upgrades" of your hero.
Put every upgrade in a upgrade-aray variable and then use this function in the trigger editor:
"Player - Set Upgrade Level Of udg_upgrades[xx] To (Upgrade Level of udg_upgrades[xx] + 1"
MfG 0siris[GoE]