The SD card slot is hardwired into the system. Not being able to print from and SD card (provided the card is good) points to a problem on the motherboard. Not being able to connect via the USB could also be a problem on the motherboard. It's the age old question of "Is it the hardware or the software?".
If you have Pronterface installed then can it connect and talk to the printer? For communication - Pronterface has a two-way interface that Cura does not. If you send M503 to the printer it should respond with it's current settings.
Can I assume that "USB printing" is enabled in Cura? It's under Marketplace and needs to be enabled for USB com's. Since it worked before this is probably not the problem but checking can't hurt.
The drivers for the USB connection are installed with Cura. Maybe a re-install will clear up the com problem but not being able to print from SD card seems to point to the printer.
OK, I have update the firmware using TM3D, same problem, but now Cura does not even see the printer.
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