Well, that is truly bizarre, I have not seen an arrangement like this before!! It would seem to be impossible for the pilot flame to reach the thermocouple when it is being directed away from it by the shield angle. I would not be at all surprised if this is the cause of your problem. On old Duotherm furnaces, the thermocouple is physically below the pilot flame, but the shield directs the flame down onto the thermocouple so it works OK.
What to do about it is another question. If your burner is like mine, and it appears to be when the pictures are compared, the assembly that holds the pilot gas line and the thermocouple is all one piece, although my vague recollection is that there may be a couple of screws underneath that would allow you to remove the shield separately from the gas line, or perhaps it would come loose when the gas line is loosened. You can remove the thermocouple easily by loosening the nuts around it, but I can’t remember if the shield portion will come out separately from its base.
In any case, the result you are looking for is that the pilot light flame should be directed forward and the thermocouple should be nearer the front of your furnace, so that you can actually light it from the port hole on the front of the furnace (which is at the lower left in the picture of the front of my furnace in my previous post). To accomplish that on your furnace, I would loosen or dismantle the shield/pilot light assembly and flip it 180 degrees so that the thermocouple is at the front of the assembly and the pilot flame gas line and shield are behind it. If you look at the picture of mine, you can see it on the right. On my furnace, I actually removed that whole assembly, turned it around and reassembled it so the pilot light was on the left of the burner, not on the right as in the picture. My pilot light portal on the furnace front was on the left, so this brought the pilot light much closer to where I had to insert the lighter to light it.
You will also need to have the shield direct the flame over the thermocouple, by removing it and turning it around if possible. If you can’t remove the shield separately and turn it, then you might have to try to bend it backwards over the thermocouple so that it directs the flame to the thermocouple. Bending the shield to be closer to the thermocouple worked for a friend’s furnace I was helping with last summer, but we only had to bend it a bit as it was already facing the correct way. I would be concerned about breaking it off by bending it too much. On the other hand, it does no good at all angled the wrong way it is now.
Please let me know how it turns out, I am interested in how it came to be this way and whether you can fix it. Have fun.