The temperatures for your prints can be controlled in the Slice Settings> Filament> Temperature.
This can be adjusted for each filament profile you are using which should automatically switch to X temp.

We have a guide for doing the E3D upgrade, but this is for a bowden setup, not direct feed.

https://matterhackers.dozuki.com/Guide/How+to+Install+an+E3D+v6+HotEnd+on+a+Makerbot+Replicator+2+or+equivalent/43

If you really want to go direct, you should consider the Titan Aero extruder.

MatterControl only has EEPROM mapping for printers running Marlin or Repetier firmware. Your printer is probably running a firmware which MatterControl does not recognize. You can still change the settings you need to, but you will have to do it by hand through the G-Code terminal. See the RepRap wiki on using the M503 and M500 commands.

@jmoody Sorry, there's a bug with the image uploads right now. 1 MB is the limit for image files, so scale down if necessary for now.

Oh, yeah, that was a great thread. I even commented on it: Derp. Thanks for the info.

Since it went away by itself, I would check, if sensor wires (end stop switches, temp sensor wires)and the hot end wires overlap. Maybe the current in the hot end wires causes some kind of interference with sensor signals.