I have the Lulzbot Prusa running off Pronterface on an Ubuntu machine and a portion into the second layer, the printer just stops. Pronterface says that it is still printing but it isn't. I think it might be the SD card reader. I pulled that off, but kept marlin the same. Could that be it? And if so, does anyone know how to disable the SD card in Marlin.

If your driving it from pronterface rather than running the print off the SDCard, it's most likely to be a problem with the USB connection.
I'd try reducing the comms frequency, and a different USB cable, one with ferite cores on either end.
I don't use pronterface, if it has a setting for verbose output, you should see what errors/warnings Marlin is throwing when it gets into the state.

I run Marlin with SDCard support and LCDSupport, on both my printers and one of my 2 printers has neither, but disabling it is just a question of commenting out the line in configuration.h.