I was finally able to install the plugin by piecing together information from several forums.
I have Plex media server running on a Netgear ReadyNAS ultra 2 plus.
This is what I did to install. (No guarantees it will work for you. )

1) Download and install EnableRootSSH
2) Download and install WinSCP (an easy to use graphical interface)
3) Download the MCM Plex agent and scanner (other) plugin at http://download.mediacentermaster.com/MCMPlex_1.01.zip
4) Login using username "root" and the admin password for your NAS (if necessary the root user password can be reset to the admin password by following the instructions here: http://readynas.sphardy.com/2010/09/res ... _4574.html )
5) Place the files from the MCM Plex plug in (other) download in the following places:
5a)Copy the "MediaCenterMaster.bundle" folder into in BOTH:
/c/.plex/Resources/Plug-ins
and
/c/.plex/Library/Application Support/Plex Media Server/Plug-ins

5b) Copy the entire contents of the scanners/common folder to BOTH:
/c/.plex/Resources/Plug-ins/Scanners.bundle/Contents/Resources/Common
and
/c/.plex/Library/Application Support/Plex Media Server/Plug-ins/Scanners.bundle/Contents/Resources/Common

5c) Copy the "MCMCustomVideoFiles.pyc" and "MCMCustomVideoFiles.pyc" files (located in scanners/common folder) to BOTH:
/c/.plex/Resources/Plug-ins/Scanners.bundle/Contents/Resources/Movies
and
/c/.plex/Library/Application Support/Plex Media Server/Plug-ins/Scanners.bundle/Contents/Resources/Movies

5d) Copy the entire contents of the scanners/series folder to BOTH:
/c/.plex/Resources/Plug-ins/Scanners.bundle/Contents/Resources/Series
and
/c/.plex/Library/Application Support/Plex Media Server/Plug-ins/Scanners.bundle/Contents/Resources/Series
6) Close WinSCP
7) Restart NAS.

Hopefully this will be able to help others having the same problem.

This all worked for me, except a few things.
I am on a Win7 pc and run the server from my pc with mounted drives from my network.
I don't have any library folders, so i had to skip those
I did all the other parts and it' still wasn't working.

So here is what I wanted to add:

go to
/c/users/(admin user)/app data/local/plex media server/
and then follow the directions for #5(a-d)

then it worked for me

hope this helps some more people

So I did all of this, and I am able to set the scanners and agents to MCM.
The problem I have is that nothing shows up when I do this, it doesn't even recognize or add anything.

What is everyone else doing to get this to work if they do use it?

Right now I just switched back to Plex files scanner and TMDB agent and put local files at the top of the list for the agent.

UPDATE EDIT:
recoded the mcm plex agent, it is now working for me. At least for my tv shows, haven't gotten to checking on movies yet.

I went through the code on the agent and updated and re-checked

It should be fixed as far as I know. Only tested on tv shows so far, but seems to work as intended.
Switch scanner and agent to: plex series scanner and personal media to find and or delete new shows.

haven't added any comments on my update, all credit is for peter for the framework, http://pep8online.com/ for code check, and http://stackoverflow.com/ for the great help and resources.

Im thinking this is not correct for a Synology. Any guides for us Synology guys?

Thank you so much for the way it was setup, it really helped me a lot. It helped me a lot.