Also, yesterday I ran a file that involved a square, the X- move was clean, but the Y-move started jittering. Then the Y-jog was jerky. The problen seems to lie in the Y-axis

Look in  C:\Mach3 for DriverTest.exe and double click on it, you need Mach closed while you do that.The driver test will then run and after a while will finish. The line on the graph should be nice and smooth with maybe the occasional spike.
Hood

If its only one axis then I would say its a hardware issue rather than software, can you swap drives from X to Y and test?
Hood

Hood, I really hate to tell you what a boner I pulled. I had the wiring all just temporarily ran "quite a mess actually" but it was so that I wasn't able to get the panel door closed. The drives are mounted on the panel door, when it is closed the drives are located right under the fan.  Steven, of SBPrecision asked me in an e-mail about the fan this mourning, so I went in and moved some wires around so the door would close. Low and behold, I ran the program 3 times with no jitter!!
 I thank you for your help and sorry to use up your time. 
Appreciatively, Jwhit

No problem at all, just glad you got it sorted
Hood