I didn't make any changes to the MDF, yet. I may still. My mods are as follows:
1) Rotate the x-axis rails 90 degrees because I had the wrong bearings. This actually works out well.
2) I don't think I am going to use the mdf x-axis plate. I am planning on using two delran blocks that are tapped. Each mounted on a piece of alum angle. One will be placed on each rail. This may turn out to really suck, and then I will use the mdf. I can't really say why, but it seems with two blocks, it it a tighter fit. It may actually bind a little, causing it to suck further. Most of my mods come from my ADD. That causes me to work way too fast and screw things up, and then I just try to work around my screw ups.
I will say this, make sure your holes are drilled accurately! Or at least oversize one per extrusion. That way you can square and parallel them. Also, I clamped my endplates together before drilling. That way they line up perfectly. (well not perfectly, but better than if I had done otherwise.)