I have updated the server to minecraft 1.9 and most of the plugins seem to be working fine now. The /heal command is not working though and I will have to try and fix that at a later date. For now if you are a donator you may have to substitute it for /feed and wait for the health to regenerate. If there are any other issues you notice, please let me know in a comment to this article.
EDIT: Buy signs at the shop also don't seem to be working.
The end has also been reset to introduce the new 1.9 features.