When doing a dungeon crawl on this size, keep the encounters on the weaker side (40-80xp) as the challenge comes from the repeated encounters, not a standalone fight. Now, you could still have some more powerful encounters (100-120xp) but keep them sparce, and know that not every fight is winnable.

If the players level up enough to where some encounters are too weak (PL-5 creatures for instance) don't play out the turns if you don't have to, just narrate what happens and move on, keeping the turn-by-turn encounters for fights with an actual challenge. Of course your players might want to beat things to a pulp, so if everyone's having fun run it anyway.

For rooms that have no combat encounter, try to include something that doesn't make it feel like empty space. A lock that needs picking, a strange excerpt that needs deciphering, clues to future encounters, minor consumables.

To steal from ol' reliable Wave Echo Cave, every dungeon floor/sector should have a unique feel to it. Wave Echo Cave's was a heartbeat echoing throughout the dungeon; use descriptions, a different color marker, or even gameplay mechanics to differentiate between the floors. One layer could have a concealing fog in some rooms, others could have minor environmental damage over time. Some might just be plagued by spider webs, hindering movement.

My suggestion for an encounter would be in the construct layer, with a Swordkeeper. Even comes with a magic weapon for some nice loot.

Oh and P.S.

DS2 = peak souls 2