Doing almost everything to figure out lag problem

I help to maintain a 50 slot server. We have quite a few plugins, and we are always looking for plugins or fixes to decrease the lag on the server, but havn't made much success. We have tried increasing the memory allocated to it but it never seems to be able to use the full 8G we give it. The upgrade to 1.4.2 R2.0 Beta seems to have taken the largest toll on the server, and don't have much of a clue why. The weird thing is that checking the server TPS using Essentials reports that the server is running at full speed, but it defiantly doesn't seem to be. Here is some info-

1. Operating System - Linux dllstx1 2.6.32-25-server
2. Architecture of OS - 86x
3. Java Version - 1.7.0
4. Wrapper - Yes, RToolkit, here is the wrapper.properties file
   
   Code:

   forced-restart-delay=5m
   maximum-heap-size=8192M
   toolkit-autoshutdown-alerts=10m,5m,1m
   restart-on-severe-exception=false
   server-saveall-period=0
   extra-runtime-arguments=-Djline.terminal\=jline.UnsupportedTerminal
   force-save-on-restart=true
   server-heartbeat-threshold=1m
   server-restart-alerts=10m,5m,1m
   minecraft-server-jar=craftbukkit.jar
   initial-heap-size=3072M
   overridden-process-arguments=
   failed-heartbeat-restart-count=5
   filter-ansi-escape-codes=auto
   severe-exception-detection-level=1
   server-arguments=nogui
   toolkit-autoshutdown-delay=0
   import-properties=false
   server-restart-delay=4h
   

5. Craftbukkit Version - git-Bukkit-1.4.2-R0.2-b2455jnks (MC: 1.4.2) (Implementing API version 1.4.2-R0.2)
6. Command Line - Running through a script I didn't make but uses the args from the wrapper.properties file above
7. Plugins -
   
8. Errors - None
9. Tried - We have had this problem in the past. We have went through every plugin and enabled them one by one, and still couldn't figure the problem. We have also allocated more memory to it. Tried butchering all mobs (as we are also having mass spawning issues), nada. The map is on running on RAM and the map still loads slowly, but it is a rather large map.
10. A vanilla server works fine. Craftbukkit is updated. Craftbukkit runs just fine. Tried added plugins 1 or 2 at a time and didn't get any results (no plugin is causing much lag by themselves, but as a mass they are lagging us. The one plugin that seemed to be a intense according to /timings was Residence, but that by itself is just fine)

If you need anymore information just let me know. Thanks for reading

 

I was just having some problems with connection lag as well. Turned out it was just a "fun" plugin I was using that a friend had examined for me and told me all the constant server sided checks that it required was putting a lot of stress on things while a lot of people were on. I'd suggest uninstalling all of your plugins and installing them one by one making sure they're up to date and optimized for a server with a lot of people.

 

Woah.
Honestly, you can probably remove half of those and your members will never notice.

There is a few heavy plugins in there.
Orebfuscator, Dynmap, MCMMO.

Also you have some outdated plugins and some that can be achieved by others on your list.
I highly suggest you stop spamming plugins and tweak them little by little.