I found the 2 remaining lines and I realized that the bleeding valve seem not to have an O-ring to replace, or it is deep down almost impossible to reach. It is definitely not leaking so I do not worry about it.
I did not realize that the high pressure and the low pressure pumps are next to each other and actually 2 separate units rather than one. Once I followed the lines I fond the the 2 remaining lines underneath the high pressure pump held in place with a small bracket.
I also installed the new fuel filter with a primer pump. This should eliminate all the air bubbles I had in the fuel lines. I think Offroakspike was wondering about my previous setup. What seem to happen was that the previous owner eliminated the connector to the fuel filter and was feeding it straight in the fuel return line. Thats why I have only 2 lines (one in one out) on the fuel filter. I kept that by just adding the primer pump to it. Got this hack from a previous CRD owner and should work a treat. The filter is a bit bigger so I had to add some spacer as well as bend the bracket so that it can be held in place.
I will keep the swirl flaps as they are till I will get an error code. At the moment the engine does not throw any, so I am ok.
Next will be the engine mount replacement on the passenger side since I have everything out and clear access to the motor mount. I got the febest inlays and will replace them tomorrow. The rubber bushings are already for 2 days in the freezer and the bracket will go into the oven for a couple of minutes. This way they should slide right in without the need of a press (I have a 20 Ton press if I need but I would prefer getting it done without).
And then I just need to re-install the starter engine and I should be golden and back on the road.
I still need to do the motor mount on the other side but that's maybe down the road when I have nothing else to do. I just want to drive this thing for once without any longer interruptions. I have not even started installing any of the mods from the V8 and it consumes more time than the V8 ever did.