I don’t have too much experience with timings, but I’ll give it a shot.
Looking at your timings, I’m noticing a clear correlation between TPS loss and entities. For example, here’s one of the higher ones:
And here’s one from where the TPS loss drops:
This trend continues throughout the timings rather predictably. Note that the number of chunks and (roughly) players is the same, so for some reason there are a lot more entities in the world. Of course, I’m sure we all know that correlation doesn’t imply causation, so take this with a grain of salt.
In addition, the timings are also identifying two choke points with saving (Nucleus’ Data Modules & Forge’s Dimension Save). This implies that you might be saving the world too often or that there’s some timings issue with saving as it’s unlikely that both are high due to separate issues.
I spoke with Ras a couple nights ago about something similar with high entity counts, and it seems that was related to world settings not being persistent across restarts (somewhat related: #1506). This apparently became noticeable when updating from 2833 to 2844, but I don’t think that’s the primary cause personally.
In the meantime, I’d suggest looking for ways to limit the number of entities in your world - there are a couple settings in the Sponge config that can help, and a plugin to clear entities wouldn’t hurt either (though I personally believe this is hiding the issue, not fixing it). Additionally (not saying you aren’t), I’d check in every day or so for Sponge updates - 2871 has an inventory fix, so for that there’s no reason not to update.
Good luck, and may the timings be ever in your favour ^^