How to completely reinstall & start over with Messages?

Messages/iChat/AIM/iMessages has always behaved spotty since I purchased a new HD and installed Mavericks on in a few months ago.
I use Messages every day: have for years, and it's running in the background, 24/7 and I use it for screensharing, teaching other Mac users (both their screen and my screen), video conferencing, even just the audio. It's absolutely integral to my business and life.
And it's really broken currently on my awesome Mac Pro:
Messages don't go through (I get the red exclamation point next to the message)
texts show up on my iPhone 5 but then sometimes they don't. Sometimes they show up on both (which is perfect)
Buddies that I've video conferenced with for years no longer can connect—this is the biggest issue. Even after installing a new Apple AirPort Extreme Base Station (ME918LL/A) in an attempt to fix this.
It forgets settings, and it often can't see USB devices (mics, camera, headsets, etc), this is even after I had the bus logic board replaced.
It even changes the font size and font name that I've selected in Preferences: Viewing (this is just totally odd)
Troubleshooting that I've done:
deleted the .plist files in both Libraries
removed all accounts and rebuilt them
Set up my AIM, my iCloud, and a GMail account, just to try and capture all protocols
the logic board hasn't been removed or flashed
I'd like to simply start over. Is there a suggested way to do this?

Hi
The .plists that might effect this are the ones in ~/Library/Preferences
I am not sure what your mean by "both".
The Airport Base Station should be using Port Mapping Protocol which works like UPnP in allowing apps to effectively tell the device which port to open.
The Preferences not staying set in the Viewing pane is odd as they are stored in com.apple.ichat.plist with all the other settings (except the Account ones that have their own .plists)
Does the Bandwidth stay set ?
Do Buddy list stay separated if you set it so in the General section ?
Does the Menu Bar icon stay on Display if the Show Status is ticked ?
To reinstall the app needs a complete OS install (Recovery mode)
However this will leave your Home Folder untouched (Same .plists will be involved).
Have you tested in another Mac User account ?
9:30 pm      Sunday; December 22, 2013
  iMac 2.5Ghz 5i 2011 (Mavericks 10.9)
 G4/1GhzDual MDD (Leopard 10.5.8)
 MacBookPro 2Gb (Snow Leopard 10.6.8)
 Mac OS X (10.6.8),
 Couple of iPhones and an iPad

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