Frankly I think you listed all the possibilities.
Exept that the cleaver can be designed properly without the need to afflict you with mining fatigue to simulate it's immense weight.
I'd probably make a new damage modifier that acts as a pre nether damage buff. Like a counter weight made of iron and stone. Would boost damage by .5 of heart for 10% slowness or whatever amount could counter one level of redstone it could be applied 3 times.
Quartz could be changed to provide a percentage damage buff from 1% to 25-30% or an amount that's balanced for the new combat paradigm.
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DFTT aside, there's a ton to be done here.
First off, shields, with different properties and durabilities. Potential rules for dual-wielding to give interesting options vs 2h or weapon and shield. An interesting and comprehensive list of different modifiers which can be infinitely more flexible than the lousy vanilla enchanting system. As a start. Damage bonus, I think, is going to be less important than other modifiers. Cleave for swords to increase their area effect, penetrating to give axes more damage vs shields, there's plenty of things to be done here.
Really, we're looking at a sea-change for combat. The Slime Knight team is not going to ignore this opportunity.