I'd recommend a RUMBA board if you can get hold of one. They're quite good, and based on the arduino/RAMPS open-source design, so will run Marlin easily. Others may have alternative RAMPS-based suggestions. These tend to be the most configurable, so you can get as much as possible of your printer operating.
For host software, I'd start with Repetier-Host, and slice with either Slic3r or CuraEngine (whichever you prefer). Slic3r is a bit better understood around here, but CuraEngine should be easier in the end. In the long run, consider buying a raspberry pi, and running an octoprint server for printing and monitoring over the net!
Replacing the extruder is a bigger job, not overly familiar with the MB design so I'd be recommending setting up a mad dual-bowden feed with an E3D Cyclops, for example... But that might be a bit audacious for now. As you research, check out E3D's stuff though, their hot-ends are well regarded/understood and in my experience very reliable.
SD3. Mk2b + glass, heated enclosure, GT2 belts, direct drive y shaft, linear bearings, bowden-feed E3D v5 w/ 0.9° stepper
Smoothieboard via Octoprint on RPi