My suggestion is to put an upgrade slot into tools (drill, chainsaw) and the sword.(only one slot) And craftable "blank upgrade" items that would be rather expensive to make, laptron crystals, maybe UU matter. The blank upgrades could then be imprinted with "programs" by expending XP levels.
The programs would act like the vanilla enchantments, allowing the use of silk touch, fortune, and/or looting. Only one "program" per upgrade.
Once you install the upgrade, it is permenant.