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!

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.