Thing-o-Matic upgrade to Sailfish/Jetty Firmware

While waiting for my new extruder (because the one I printed myself physically broke before I was able to print my improved, stronger one), I'm upgrading my Thing-o-Matic to the Sailfish firmware everyone is talking about.

First step was to solder the Interface Kit that is collecting dust since at least 2 years.
I did solder some buttons 180° reversed but they work nonetheless.
Interesting fact: The display is black while USB is connected but fine without USB.

Next step: Download and unzip the software.
...takes ages on an old Atom based EeePC despite my flash disk upgrade.

After updating to "MakerBot Motherboard v2.X(Gen4) with Mega 2560" the interface reacts extremely slow and I can't connect via USB anymore. (Solved, see next issue below)
Serveral seconds to register a single key press on the interface kit.
Rebooted the PC, now I can connect but it can't find Toolhead #0 and the console is full of "timeout" messages.
Consequently I can jog but not turn the ABP gelt or move/heat the extruder.
My versions:

• Thing-O-Matic with an MK6 extruder (no MK6+), ABP and Gen4 interface kit.
• ReplicatorG-0040-windows-r003
• "MakerBot Motherboard v2.X(Gen4) with Mega 2560"
• Sailfish Firmware v4.1 (r720) 
• Extruder Controller v3.6, AtMega168 (was way too small to read at first.)
• Update: Extruder control firmware now 3.1

Update: Forgot to open cable hell, dismount the extruder control board, so my angled USB plug would fit and upgrade the extruder firmware. The step was not mentioned in the installation manual.
Much faster now, toolhead can be manipulated.
The firmware of the stepper controller is not updated through it's connection to the main board.

New issue: Display width smaller then firmware thinks it is. Extruder and bed do not heat. (solved)
...this is going to be a loooong night.
There is also a problem with ReplicatorG that luckily is of no consequences here. The list of machine types is longer then the display and does not scroll.

• Update: Found a setting "onboard prefs"->Motherboard->Misc where the display is set to "20x4" while it is "16x4" 
• Problem: That dialog is smaller then the screen(1024x600) but the "OK" button is outside the window (I can barely see it's upper corner) and the window cannot be expanded in height. Only in width. 
• Update: I was able to create a virtual display 768px high and the upper 4-5 pixel rows of the button became visible.

New issue: Display blank when USB plugged it while switching on ToM. Can I move the extruder stepper forward/backward, Belt and jogging controls on the PC now failing.(mostly solved)
Jogging works find on the interface kit, without the PC.
Control Panel in replicatorG suddenly also stopped to display the target temperatures in the graph. Only the current+past temperatures are graphed.
I can move all axes and heat up via the interface kit but not move the extruder stepper forward/reverse.
power-cycled the ToM. Display now stayed on while USB but the offset display ha returned! (Aren't onboard preferenced saved in flash?) ReplicatorG hangs when trying to disconnect to connect anew.
Set display size again, rebooted the ToM. Now all except the extruder forward/revers is working. Why?
After trying to extrude with 1,89 RPM jogging is failing again.
Then jogging resumed, and failed again. It looks like axis-jogging is disabled while it thinks it is moving the extruder (wich is not moving at all).


Last issue: Extruder stepper not moving.
One of the extruder cables had come loose while checking the print on the ATMega168 (to make sure it's not a 368). No changes. Extruder stepper still unresponsive.
Flashing the extruder firmware 3.1 again. Failed. Powering down. Unplugging USB. Trying again. Flashind succeeded.
Issue persists. Extruder stepper does not move and machine has forgotten it's onboard preferences yet again.
Checked the extruder cables. Everything connected correctly.
Tried to uncheck "volumetric 5D extruder" but it did not help.
The DIR LED is glowing but the STEP LED on the extruder controller is constantly off. So this may be a software issue.The fan of the extruder is also off.
I can hear a very faind "thud" noise when pressing "stop" after forward or reverse. So something is happening.
I found this but there is no "extruder hold" in the "misc" tab. for "ThingOMatic w/ABP and Extruder MK6 (Accelerated)".
With "ThingOMatic w/HBP and Steptruder MK7 (Sailfish)" I can disable "extruder hold" and get at least a high pitched sound when the extruder stepper is supposed to be running. However still no movement.
I mistook the heater cables for the extruder stepper cables.
Will test extruder stepper cables and switch axis A=extruder with X and jog on Monday.
If that works, it's clearly a software fault. Question is...what to do if it is?
Solved! It turned out to be a hardware issue.


....(still updating this blog post)

• Google+ posting
• Software Download
• Firmware installation guide 
• Host software setup guide
• Firmware support group