We seem to have found the causes of the lowered TPS; And have hopefully have alleviated it to some degree. If you know of someone or something that is causing the TPS to decline. Please don't hesitate to tell a moderator, so we can try to make the general playing experience more enjoyable for you the players.
Does leaving 64x64 quarry holes filled with endless flowing water cause issues? I mean, I know it won't when chunks are unloaded but if people are hanging around... we've reported this to a mod a few days ago and were told this was not a problem and there are no rules against leaving flowing water in quarries. FWIW I always drain mine as it was a rule to not leave flowing water on the lagcraft FTB server and it is just a habit now.
TBH it's not that big of a deal because there a normally much bigger problems that lower the TPS then just water. If it was a bigger then 64x64 hole(Maybe quadruple the size); Then maybe you might need to be slightly be worried. But until I haven't seen it cause any issues from 1.1 to now, so you shouldn't have any issues with just leaving it.
Water is not a problem. Vanilla features tend to be considerably better optimized (especially with what we use) than compared to anything a mod does. If something specific is being a problem, we'll be sure to mention it to everyone if we can't fix it.