Well I am having MUCH better luck with the 1.2E update! I guess a lot of my issues were related to the fact that I was only using the Amiga in HighGFX mode. Now that the config tool works in HighGFX mode all my changes stick! The screen centering on my LCD still isn't perfect, for instance in 1024X768 I am forced to miss 3 pixels on a side of my choosing but a lot of that is probably due to the monitor I am testing on. I was also able to get a decent pixel clock sync with my monitor adjustments unlike with 1.2D.
Default PAL config syncs perfectly for gaming by the way! But I may have to try 50HZ mode connected to my multisync just to see if it is smoother.
Thanks again, things are looking good!