I rebooted and as soon as the screen came up I clicked System> System Log so I
could see if anything was being posted. I can scroll the syslog screen but I
cant click on anything. Lost control pretty much immediately.

I have six usb ports so I started moving my mouse and keyboard around to the
other ones. None of the ports in the back seem to allow me to click on anything
but I can move the mouse and scroll. And the keyboard can sometimes activate a
item (clicking enter).

I just discovered that the front usb ports though are working for both my
keyboard and mouse and I can click on things and work again. But how do I
trouble shoot the rear ones?

It's not a usb 2.. 1 problem is it ?
Sometimes the backports are usb 2 and the front ones are usb 1.

You could try a couple of things to check you don't have broken
packages though,
Drop to a console and try sudo apt-get install -f
if there is a broken package this should find it.
Then try sudo dpkg-reconfigure -phigh xserver-xorg

The other thing that may just get it going is
sudo dpkg --configure -a
Failing that you could bite the bullet
and
sudo dpkg-reconfigure -a
Pay careful attention to what you are doing if you choose the last option
though as it basically fully reconfigures your system.

If you have a live CD, one which will boot without installing a fresh operating
system (such as Ubuntu)boot from the CD and see if the system responds more
normally to mouse and keyboard. If it does you have possibly got a data
corruption which could be due to a failing hard drive or an electricity supply
sisk.
If you do have a live CD save your data ASAP.
If the keyboard and mouse don't work normally with the live CD you might have an
incipient processor or motherboard problem.

Wouldnt that show up on all usb ports and not just one(set)?

My /home is on a different drive - thankfully.
My os is on a brand new drive - not that that means anything :D

Running lsusb I show 8 usb ports.
I have actually six.
Shuttle specs say I have two front and two rear 2.0 ports and two 1.1 ports.
However, when I plug into all of the six ports, none of them are 2.0 usb ports.

It might be the motherboard.