After 1 day of running this so far, my players now report that they haven't seen a single bit of server-side lag all day
I will try running the server for a few days straight soon and see how that goes.
The first bug I have found so far is that one of my quest NPCs in PoTimeB was shouting that Crushbone was going to reset and it reset PoTimeB instead. The zone resetting NPC in potimeb is definitely only set to reset potimeb and only set to warn that it is shutting down that zone. Crushbone has a completely different quest with it's own spawn that shouts about Crushbone being reset.
When I first put the quests in, I had all of the timers set to the same names in each zone and I think this may have been the problem. All of the timers were $reset, $warning1, $warning2, etc. Now, I have renamed each of them in the quests for each zone. For example, Crushbone timers are now called $cb_reset, $cb_warning1, $cb_warning2, etc. I will test and see if that clears up my problem.
The only other thing I suspect that might be the cause is that I used 1 NPC type for all zones. I used GeorgeS' tool to setup 1 spawn that spawns in all of my custom zones. You just add a line under "Spawn2 Spawn Locations" section and set which zone you want it to spawn in. I added 1 line per custom zone I have and them all set to spawn from the same "Spawn Entries" NPC. If the change to my timer names doesn't fix the problem, I will just make individual spawn entries for each custom zone instead of 1 for all.