All

Just some facts about Omega D enlarger alignment.
First and foremost. Proper alignment begins with proper assembly. And from the
dialogue here there are some assembly problems.

Next. The eccentric rods, wherever they are located, are to align the carriage
proper to level the negative stage supports. Fore and aft. Not too much is
available to align left and right except proper assembly. Make sure the nylon
screw sliders are centered to allow the carriage to travel smoothly. All should
have about the same adjustment.
Next the negative stage "bridge" needs to be parallel with the baseboard. The
most critical part of the alignment after proper assembly.
You will almost have to take what you get for lens stage adjustment. There are
no dedicated adjustments. The vertical brass rods and their supports can have
excessive wear and their replacement or disassembly and reasssssembly will
occassionally do some good. Again proper assembly. Cleaning is also important
here. Severe focus shaft support can be a problem. Nothing to do here except
mill out the slots and use bushings to get back to original.

Lens stage alignment is not really that critical if you consider the procedure
to determine actual focal point of the lens.
 
At this point you have done all you can for the mechanical alignment of the
Omega D enlarger. Next is the optical component(s) and their integrity. A
properly mounted lens  on a lens disc is really simple. Again proper assembly
is most important. At this point you are dealing with the integrity of the lens
itself. And this is beyond most of us.
Bob  AZ