(Note: I'm willing to compromise on some of these concepts as they're fairly rough ideas.)

So, here's my scheme to allow for customizable difficulty!

Basically, these would be craftable difficulty mods called Clockwork Cartridges. I'm thinking there would be three variants. One with a one-star cost that has 3 uses, One with a two-star cost that has 12 uses, and one with a three-star cost that has 50 uses. Ingredients would either be materials relevant to what the individual cartridge does, or using the minerals to fit in with storyline reasons.

The cartridges could be submitted upon choosing a gate. Only the first person needs the cartridge to make it active for all party members, but they must all permit to the use of them to make the cartridges active. They would alter certain aspects of the floors as you proceed, allowing you to make the exploration a little more challenging. Perhaps a score system could be added with the cartridges acting as multipliers, something that can go on a leaderboard or just possibly a player's profile.

Cartridge Ideas include....

Cartridge 1 - Berserker: Enemies within the Clockworks take more damage from your attacks...but they deal a lot more in return!

Cartridge 2 - Danger!: Enemies throughout the Clockworks all act as if you were in a danger room (So, one stratum/tier higher than where you presently are

Cartridge 3 - Status Sensitivity: Players suffer status ailments for a longer length of time.

Cartridge 4 - Shield Master: Shields drain instantly upon use. If you want to defend, you have to time your shield raising!

Cartridge 5 - Clockworks Mystery: all Floors are hidden. You won't know for sure what you're getting into!

Cartridge 6 - Armament Roulette: Weapons and Armor change with each floor randomly. (Probably something like 0 Star equips for Strata 1, 1 Star for Stratum 2, and so on.)

Cartridge 7 - Eternal Haunting: the Phantom Knights from Graveyard areas will appear on all floors.

And some options for the true masochists....

Cartridge 8 - Hardcore Mode: You have one life. If you are brought down in combat, you are automatically taken up to Haven, your spoils of war forever lost to the mysterious clockworks...

Cartridge 9 - Endurance Run: All 29 Floors of the Clockworks act as Tier 3 areas. You are only able to leave the Clockworks from Terminals and the Between-Tier areas. If you die, you have to use energy to revive if nobody can pick you up. (If you have none, you will be allowed to go up to Haven, but only if you and everyone in your team are unable to revive through any means, but much like in Hardcore, you will lose anything you picked up.)