Hi jeff,
Congrats for finding the *.json file, it took our experience of printing to another level, there are some unfortunate design problems in the way it is designed but it trully enable you to get much better prints.
We are using the custom profiles to print dana bloom jewelry and as you can see her jewelry do not have the regular engineering design so are not so simple to 3D print.

The problems that I hope someone in Makerbot (hopefully this thread has drawn their attention) will fix someday and will sure make my life and anybodies else who uses Makerware are the following:
Speed,Support,temp and raft should not be controlled in the profile or more exact: those setting in the profile should be able to be overwriten as in the standards profiles.

Regards,
Assaf
3d Printing Center Israel