MakerBot Print is our newest print-prepration software, which supports native CAD files and STL assemblies,
allows you to interact with all your printers via the Cloud, and many other exciting new features.
I remember someone having the exact same problem with another thing. Could it be you're using a Pro Mini clone with an ATmega168? The Pro Mini should have an 328P but the 168P ones come with only 1 KB of SRAM.
Try commenting out all "Serial.println" stuff you see. Should only be 2 or 3 lines and this should save enough memory to upload to 1kb.
Edit: Try commenting out the following lines:
105 - 107 (serial.begin and 2 lines with serial.print in void setup())
261 (entering setup mode in setupClock())
307 (setup done in SetupClock())
That should get you down to about 860 bytes memory usage.