I'm a bit surprised by the difficulty you ran into. I've done several of these, the longest was the first on an M103 where I followed the book exactly, and it didn't take more than a couple hours. However, I must admit I had all the tools. The last one I did was on an M104 in a C280. Much tighter than a 124 E Class. That one went fine without removing the P/S Pump. Two real oddball things:
1) I have never seen one of these engines without the hole for the fan hub locking tool. Are you sure you didn't miss it somehow? Sometimes it is difficult to see, especially on an M104.
2) I can't figure out what the extra "O" Ring was for on the pump. Normally it is one for the pump to block and one smaller one for the heater pipe. But, I can't figure out how the pipe is bolted to the "manifold". The pipe usually runs across the front of the timing cover and connects to a hose. Are there two heater pipes?
It does sound like your pump was fastened to the block with conventional capscrews rather than socket head screws, which would be somewhat unusual for an M104.
At any rate, this whole thread may help someone else in the future