How to setup MAKERWARE for Taz 4??

I had printed a skull on a Replicator 2 a little while ago. In the pictures it is the dark skull on the right and it came out beautifully with almost no finishing needed to be done except for the back. I really like the way it printed the supports as well as the initial layers that are crisp and clean. The same cannot be said for the print I got out of the Taz 4 which is the white skull on the left which was sliced with Cura. The inital layers are pretty ugly and there are a lot of rough bits and pieces throughout the print. Both of these were printed PLA. The Lulzbot printed at 210 degrees and the Makerbot at 230 degrees.
I figured I want to do a side by side comparison of the same slicer and want to get a Makerware slice to run on the Taz but I am running into some issues. As you can see in the Printrun image the object is placed outside of the build area yet in Makerware it is centered. I finally got it on to the build area by moving it way to the upper right outside of the build area in Makerware. However when I then go to print the printer does not Home and it begins to print with the Z about 4 inches off the build plate and quickly reverses the filament. Does anyone have any suggestions on how to get the GCode from Makerware to work for the TAZ. Anything would be great.

Thank you!!