After publishing this Instructable and using the setup for a while I have a few more tweaks to post.

First is that to enable the SD Card you have to uncomment the #define SDSUPPORT around ln 1120 in Configuration.h to be able to print from the SDCard. There is also a #define SPEAKER too to use the speaker next to the knob.

I also discovered the default direction and steps of the rotary encoder were kind of wonky. You can still get around but it doesn't exactly behave as you'd expect with respect to direction. For the LCD that I bought I needed to change the direction of the encoder and the menu to get things to move in a logical direction. I also added individual axis homing.

uncomment #define REVERSE_ENCODER_DIRECTION

uncomment #define REVERSE_MENU_DIRECTION

uncomment #define INDIVIDUAL_AXIS_HOMING_MENU

Printing higher temperature filament like ABS would trigger the max temperature fail safe so I had to adjust that to a higher temp. I chose 260 in Configuration.h with this line.

#define HEATER_0_MAXTEMP 260

I upgraded my extruder assembly with this all metal one (http://amzn.to/2omeYEI) and the gear was a different size so I had to adjust my extruder steps. I extruded and measured filament several times and did the math to zero in on 99 steps for my extruder and gear and updated this code in Configuration.h to reflect that:

#define DEFAULT_AXIS_STEPS_PER_UNIT { 93, 93, 1097.5, 99 }

The heater bed in the Mini isn't the fastest at getting up to speed and I found that Marlin would detect an error happened fairly often so I increased the time it waited to detect a problem a little with this line in Configuration_adv.h

#define THERMAL_PROTECTION_BED_PERIOD 45 // Seconds

Lastly I printed the parts for this LCD Cover http://www.thingiverse.com/thing:2133588 and moved the LCD into the machine. The pints on the bottom of the new controller didn't fit the pins of the Monoprice controller so I found some bushings to attach to the bottom of the Arduino Mega to keep the pins off the metal plate and found a enough space to put everything in and re-attach the bottom plate.

I have a Raspberry Pi mounted on the back of the printer that I use Octoprint with to control my printer. I drilled out a hole in the back by the power connector to run the USB cable out of the new controller up to the Pi. If you make the same modification I would disconnect the whole controller and move it away from the printer to make sure you don't drop metal shavings into your new controller.

After all this the printer is back in business. And to be honest I think it prints better prints than before and there are more protections from thermal runaway in the Marlin firmware than the one that shipped with the Mini.