Top surfaces rough

So I finally got my 1.0a bed leveled as perfectly as I can, after switching from the manual leveling option in repetier .92's menu to the method listed in the bed leveling for beginners thread.

Now, I've got a new problem though.

http://imgur.com/sWXSO91
http://imgur.com/18nX7Z2

I've gotten suggestions that it's overextruding. I have doubts that it's that, since before I tried the new method of leveling I was making prints that didn't have this issue. I've tried lowering the extrusion multiplier just in case, and it doesn't have any effect on the roughness. I just end up getting more holes in the side of the print due to not extruding enough.

I thought that maybe the nozzle was just too close to the bed and it starts tearing through the print after a certain amount of layers, so I added 0.3-1mm to the z offset. That made it so that the nozzle was too far away, and just squirted out abs into the air.

I'm so close to finally having my printer in working order again...anyone know what could be causing this?