For adding a new armor upgrade? I wish to make some Terran-trained zerg from a special structure. I may use a special building for the structure, and i may need help later implementing it's ability to train zerg, but the primary question: Can I use the unused upgrades to make "Reinforced Carapace" and "Reinforced Zerg Weapons"?

You can. Set the armour or weapons in DatEdit to the unused upgrade(s) in question and use Firegraft to let players purchase the upgrade.

^ Those armour and weapons would be essentially a different "class" though. You would not be mimicking the effect of something like the Ultralisk's +2 armour upgrade. (Just a note.)