I do not have a fan permanently mounted but i  have a 120mm fan, connected to a pc power supply, blowing on the board.

I have previously loosened the stop nuts and adjusted them to make circles more round but I will give it a try again and check the VREF also.

VREF's can be tricky it's a trade off to low they skip but are  nice and quiet to high and they get noisy and can still skip. They really just need to be just right.  Focus on the mechanical smoothness first it really doesn't take much to bind things up.  Do you have a fan blowing on the printer board?

Well it didn't do it as badly but still isn't good.

That's no good.  Have you loosened the set screws on the belt to motor pulleys or remove the belt.  Then move the extruder front to back by hand to feel if it travels smoothly?  Also the VREF could still be slightly off but you need to check for smooth motion of the mechanical side first. 
Those side belts need to be aligned with each other by loosening the set screw on the drive pulley so it can rotate freely on the rear Y-shaft.  Then adjust the tension of the side belts equally.  Then tighten the set screw on the left side first.   Move the carriage front to back until the right side feels like it is resting in a nice neutral position and tighten the left setscrew.  Then check for smooth operation of the Y- Axis and repeat if necessary.

definitely the 2nd board except it is green.  I plugged an old 120mm fan into an old power supply and set it on the counter behind the machine.  I have it printing the last design it messed up on.

fingers crossed?

Here is a Sanguinololu

Here is a Printrboard

Notice that the Printrboard doesn't have plug-in type steppers like the Sanguino.  On both boards you can adjust the voltage (vRef) using the little trimpot.  Adrian has posted a tutorial on ho how to adjust the vRef and the values you should adjust to.  Do a search for vRef adjustment or tuning.

Even without that reference.  Try adjusting the "Y" trimpot clockwise just a little, 1/8th of a turn, and see if it helps.

I was reading on another thread and they mentioned the motor being a little week for the job.  Is that something I should look into replacing? 

The printer is being used in my Jr. High Computer class and repairs and replacements will probably have to come out of my pocket.  It is too hard getting the school district to do anything.