Makerbot Mini Alternate Firmware

Hello, I am having two separate issues with my simplify 3d software interacting with my makerbot mini.

I contacted Simplify3D support and they said that it could be due to the default firmware that my Mini has, anyone know of some alternatives that I could use for the firmware? Does something like Sailfish work with a Mini and Simplify3D with the features I am missing?

It works perfectly fine with the lulzbot I am also controlling from the same machine but when I am using the Mini I have some issues. It will print everything perfectly, but after a successful print is completed I need to restart my mini printer to be able to get it to reconnect to my computer. It will show up under the machine control panel as a port option but will be unable to connect. If necessary I can provide screenshots of this.

Second is that I am having a problem where I can't manually set the extruder temperature from the machine control panel. When it is connected I press the Set button but nothing happens even if the target temperature is set correctly on the left of the current temperature. I need to be able to use this feature to be able to safely change out filament from my printer without having to go back to the makerbot print software. I tried to use gcode to fix do this manually but I get an error saying that it cannot open plaintext gcode files due to the firmware

Any tips related to my issues would be invaluable, thanks!