First question is: do you have LED tail lights in your trailer? If so, read further...
I have a 2008 GL320, and I had a similar headache. The vehicle didn't come with a receiver, so I installed the OEM unit and the wiring harness, and then couldn't get the lights to work. Bought and installed a new SAM, as that was some conventional wisdom from one of the MB forums, and I doubt that made much of a difference (the new SAM cost about $200 as I remember, but I installed it myself). The thing that I eventually discovered is that my trailer's LED lights did not have enough resistance to convince the SAM that there was a trailer connected, so it did not send the juice to the lights, or recognize the trailer being there. You can buy adapters that have a resistor installed, but I bought some resistors to put inline with the trailer's wiring, and voilla--it started working as it should.
The brake controller was then another headache, as my vehicle did not have pre-installed (if there is such a thing) brake controller wiring. I did find instructions for doing my own wiring job, but was growing weary of the whole experience, so bought a Tekonsha Prodigy 3 (?) wireless brake controller.
I have racked up a few thousand miles using this brake controller, and am happy with it (though I still feel like I would be more comfortable with a hard wired arrangement). It is about 3x more expensive than a conventional controller, but then I suppose it is a matter of what my time and frustration is worth.
So...What you have done seems out there in the realm of the wild west (in MB world, at least). since the "recognition" of the trailer being attached is managed by the SAM, and you have essentially bypassed it, the vehicle is blind to the knowledge that the trailer is back there. So I can well imagine that you aren't going to get power to a brake signal, and the adjustable vehicle height (if you have it) will work (whereas it should not), and who knows what other black box issues may arise (ie., are the shifting points changed when there is a trailer?). The fact that you can send a manual brake signal, but not an "integrated with the brake pedal" signal tells me that the vehicle isn't sending the signal because it doesn't think there is a trailer behind the vehicle.
Sooo my recommendation would be to restore the original wiring, and put a resistive adapter between the vehicle and the trailer and try to get the lights to work "as designed." IF all else fails, resort back to your jury-rigged wiring and get a Tekonsha Prodigy wireless controller.
There are several threads on these forums about getting european tow vehicles to work with these trailers' lights--try searching for "Mercedes lights" and various permutations and you will probably get some hits.