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Pf2e actually does have a dedicated disease mechanic, which is essentially to structure the affliction as a set of stages with defined lengths. At the end of each stage’s length, you make a new save against it, and reduce the stage by 1 if you succeed or increase it by 1 if you fail (2 if you critically fail). Here’s the existing diseases you could copy from, including for example malaria). In most cases pf2e’s DCs are scaled to the level of a creature or effect, meaning that a level 1 character has about the same chance of beating a level 1 DC as a level 10 character has at beating a level 10 DC. What that means though is that +1 and -1 bonuses are pretty strong, and inflicting the kinds of penalties 5e’s exhaustion has would probably quickly lead to a TPK. Hope that helps!
Afflictions - Rules - Archives of Nethys: Pathfinder 2nd Edition Database

Diseases and poisons are types of afflictions, as are curses and radiation. An affliction can infect a creature for a long time, progressing through different and often increasingly debilitating stages. The level of an affliction is the level of the monster, hazard, or item causing the affliction or, in the case of a spell, is listed in the affliction entry for that spell.

Pf2e workbench is a must-have, it comes with a bunch of macros (especially the Basic Action macro that bundles up a bunch of the other basic action macros into one menu) and other automation.