1 and 2 sound like Smoothie problems and not anything specific to the Kossel. You might find better luck asking the Smoothie guys about those. They are pretty helpful and active on the Smoothie IRC channel.

1. You need to find out what is causing the halt condition. Have your printer connected to a computer with the terminal window open, then send it a reset command. It should report any errors through the terminal. Most likely, there is something wrong with your config or something is not wired correctly. After you send the M999, it is normal for lights 2 and 3 to blink. This indicates normal operation.
2. Again, this could be a config error or just something is not connected right. This may be related to problem 1. Double check your connections on the wiring diagrams from Panucatt.
3. I would get the other problems sorted out first before you deal with this. Have a look at this guide on dealing with temperature issues.

If you need to upload your config file, use a service like Pastebin.

MatterSlice is the only slice engine supported on the MatterControl Touch tablets. CuraEngine and Slic3r do not run on Android.

Version 1.7.1 is extremely old now. I'm not surprised that it doesn't work. Unfortunately this is the latest version available for Mac. If you have another computer with Windows you can try 2.0. Otherwise you will have to wait for the 2.0 Mac release.

You just run mattercontrol from the terminal (all lowercase) or find the MatterControl shortcut in your application menu.

The path of the actual executable file is /usr/bin/mattercontrol. MatterControl is a Mono application, so yes the files with the .exe extension are correct, even on Linux.

AFAIK, MatterControl has never been packages in Ubuntu's repositories. I don't know how you were ever able to install it through that method.

The file is not actually a .tar.gz file. It is a .deb file. I'm not sure how it is getting the wrong extension in your case. All you need to do is rename it to MatterControlSetup-1.7.5.deb and then install it as normal. You can also just download the .deb file directly from https://www.matterhackers.com/store/l/mattercontrol/sk/MKZGTDW6.

MatterControl now splits up large moves into a series of smaller ones. There are a couple reasons this is done, but it ends up having the effect you are seeing. Is this a problem?

Sorry, its not setup to work on Linux. It's looking for avrdude.exe as if it were on Windows. I'll file a bug report. In the meantime, you should be able to make it work by installing avrdude as you normally would on your distribution, then make a symlink from /usr/bin/avrdude to /usr/lib/mattercontrol/avrdude.exe.

If you were logged in to your MatterControl cloud account before, then all of your printer profiles and settings will be restored when you log in again.

Otherwise, everything is kept in the application data folder, which is in ~/.local/share/MatterControl on Linux and Mac and C:\Users\{user}\AppData\Local\MatterControl.

Turn off the Center On Bed option.

http://wiki.mattercontrol.com/SETTINGS/General/Output_Options/File_Settings/Center_On_Bed

This is where the rotation controls are.

http://wiki.mattercontrol.com/3D_VIEW/Edit#ROTATE