I had trouble with my prints being too far to the right and too far back on the build platform. There were 2 fixes that solved this problem.
Solution 1 - Fixing the rest position.
If your makebot is doing a slide backwards before it waits to warm up (like mine did) you need to fix the start.gcode. There are several solutions. My choice is to remove the X and Y coordinates on the line that has the (move to waiting position) comment.
Solution 2 - Fixing the stored position.
Plug in your Makerbot, open ReplicatorG choosing "Machine->On Board Preferences". Fiddle with the X and Y axis offsets in the first tab and do test prints until you're satified with the orientation. Forget about the script, it doesn't work.
(I've mentioned all these things in a previous post but had a hard time finding it because I didn't use good key words. Hopefully this will help someone else find this information.)