Didn't took me to long to install all parts but I was searching for the (in the instruction mentioned) extruder assembly and gave up after searching a while because it worked at first. Now I'm running into some problems and did see you make a photo I've never seen before. Is there any link you could provide? I'm sorry if this is stupid but I'm just not able to find or see it anywhere... ):

Seems like I'm having similar issue. It seems like MMU2S and Extruder are doing tug of war after few seconds of loading filament. I couldn't pinpoint which MMU2S or new Extruder that caused the issue.

I know this is an old post, but I wanted to reply because I experienced this also. It seems if the MMU2S tensioning screws are too tight, the MMU2S idler won't rotate to the correct position and remain stuck on a bondtech gear when it shouldn't be. My solution was to loosen the MMU2S tension screws just a little bit. Instead of their heads being just below the surface, they are level with the surface. The tug-of-war problem stopped. The MMU2S seems incredibly sensitive to the tightness of these screws.

Bypass the MMU, you should be able to print as a normal MK3 if the MMU is not working properly. 

Thanks sneaks, I'm starting to think this will solve my problem also....however, I can't print it...catch-22...sigh.

I thought Id just quickly share my solution to this as it might help someone without altering the shape of any parts.

I think I had sort of the same problem. Basically no filament ever left the MMU. There was low resistance and loading was otherwise ok. Was sure I had the sensors nicely tuned, but turned out that the IR sensor startet triggering from the movment of the bondtech gears in the extruder as soon as the MMU started to load to nozzle. So the loading stopped, naturally. I wasnt able to detect this when trying to calibrate the IR. 

To solve it I simply moved the tower as far left (away from the door) as possible, and tightened  it really good in that position. The IR was 1 wihtout filament then. Then I tightened the spring loaded screw until the sensor went to 0, and then even som more and way more than the manual says. 3-4 threads outside the nut. This holds the door tightly fit and allows the bondtech gears to move without triggering the IR. Havent had any trouble with filament not going through to the nozzle since.  This is on MK3S MMU2S with latest firmware using prusament pla. Havent tried other materials yet. Crossing my fingers this wont give me other problems later on, but it wouldnt surprise me :)

Good luck

If I help the MMU with putting the filament to the printer there is no problem with printing.

So I now only have a bondtech mmu issue how can I get this resolved ?

As today, I finally managed to get calibration corrected. I noticed the MMU2S first print calibration is different from my new MK3S - filament seems smaller than MK3S. 

My next target: get all 5 filament in and see if it worked correct. But that will be next weekend - I'm bit busy with real life. 

Nothing I can say would ease your pain. Been there and understand what you're going through. The chimney design with the IR sensor need to be perfectly adjusted. There is no space for any errors. So first of all make sure the IR sensor is not moving by itself. The plastic cap doesn't press it down like it should. As the next step make sure the sensor triggers after around 0.75mm filament width is inserted. Otherwise you might get fast back and forth switching values during operation and load/unload. To make it more complex make sure this is happening with correct idler screw tension. Be prepared to adjust this if needed. This is something you might see during first prints.

This is the most important step in the whole MMU2s assembly. If this sensor is not working correct, you will get very strange and funny errors. It decides if the MMU2s will stay on the printer or put back in the carton (in rare cases even further).

I will work on it tomorrow along with all 5 filament test - I will put the modified version on it. 

But the sensor test kept changing "0" and "1" if I sightly touched the chimney.

Did you try my modified version of the idler door?  I redesigned it because I was having the exact same issues.  The modified version fixes it by moving the pin for the gear .75mm closer to the door and reducing the size of the area surrounding the pin so it has more clearance for closing.