Under Construction
At the moment, this is a work in progress. I am currently going to be documenting the tuning of my Ecksbot 2014 process here.

Step 1 - Marlin Firmware 2.0.5.3

The best thing to do first is to setup the firmware for your printer. This will allow you to control it from your computer so you can start calibrating things. For this you will need several things including the Marling firmware and the Arduino IDE software.

Step 2 - Octoprint

cd ~
sudo apt update
sudo apt install python-pip python-dev python-setuptools python-virtualenv git libyaml-dev build-essential
mkdir OctoPrint && cd OctoPrint
virtualenv venv
source venv/bin/activate
pip install
pip --upgrade 
pip install https://get.octoprint.org/latest

//replace username in place of pi below
sudo usermod -a -G tty pi
sudo usermod -a -G dialout pi

Step 1 - Adjust the X-Y Axis Spacing

The first thing to do is to adjust the spacing between the Y axis rods (front to back rods) and the X axis rods (left to right). You can use a micrometer if you want or use any item that is of fixed length that is long enought o touch between the Y and X axis vertically without the hot end touching the bed.

From the rear of the printer move the bed all the way to the front so you can expose the Y axis rods. This exposes enough spacing between the Y axis vertically to the X axis so you can insert a spacer there. The goal is to place the spacer between the Y and X axis on the left and right rails and adjust the threaded Z threaded rods by hand until the X just touches the space. Once you've done this, both Z axis are the same distance physically from the Y axis meaning the X and Y are in alignment.

From this point forward do not touch the Z threaded rods as this will throw the axis' out of alignment.

Step 2 - Adjust the Bed Height

Your bed may have 3 or 4 mounting botls that are ajustable. Mine has 4.

First, make sure the nozzle is at least a little above the bed so as not to touch it as you move it around. Use the controls in Repetier (or similar) to move the Z axis up or down as needed to make sure you clear the bed.

Next, click on stop motors, then physically move the hot end so it is above one of the bolts, then lower the Z again using Repetier until you can see just a little tiny bit of space between the hot end and the bed. Now slowly move in position over the other bolts to see if the spacing is the same above all the mount points. If it is then you are a lucky person! If not, the beds needs to be levelled.
Be aware that some beds can be twisted, bent, you name it. You can put the edge of a straight ruler across the bed in different directions to check this. If it is damaged there are ways to compensate for that (auto or manual bed levelling) but you still need to do this procedure to get the mount points all at the same height.
If you have to adjust your bed heights, first you need to loosen every mount point. Then you can choose the first mount point to adjust until a piece of paper just rubs between the hot end and the bed. Next do the same for the opposite coner to the first one. Then do the third. If you have a fourth, do it once the third is done. Verify they are all a paper width above the bed then lock down the bolts carefully whilst checking and rechecking the spacing.

Step 3 - Adjust Z End Stop

Now all is left is to adjust the Z end stop. On mine it's a bolt that touches the mechanical end stop.