Done The Lag Stabbings of 2015

I got 60 FPS in your base so I can't profile it.

What you can do is:

1. Download VisualVM
2. Start minecraft and log in to the server
3. Start VisualVM and double click on: http://i.imgur.com/34uo7ty.png
4. Switch to the tab Sampler and click CPU
5. Let it run for ~5 minutes then stop it and click on Snapshot http://i.imgur.com/jxNFPQa.png
6. Click on "Export to..." (First icon), save it and upload it

 

Create a zip file

 

3 Ways to Make a Zip File - wikiHow

 

ugh, please export it as nps

 

ty, that's good.
I just logged in order get a snapshot for comprehension. Unfortunately I noticed that I have lag spikes, so I read the first post closely and noticed that this is the issue for you. I thought it is permanent.
The bad thing is that the profiling does show the average. Though I tried to catch those lag spikes with thread dumps but I wasn't able, too. They were just too quick.
I have no idea what else we could try.

As last resort, did you ever think about moving? If you would move one thing after another and watch closely you might be able to figure out what it is.