Ha! Made it to twelve posts, so I guess I can show photos now?? I'll give it a try:

imgur.com/a/js3Yb6j

Here you can see some pictures right after the moment I bought this beauty up to the current status. 

I've pretty much finished the bike, just a few minor improvements before I can take it to the track and run it in.
There's one thing left that irritates me:
In the service manual you can see ignition timing marks on the flywheel as well as on the pickup. But I don't have the mark on the pickup. I didn't change the timing yet, just built in the stator and rotor and when I go to the desired timing which is 2.0mm BTDC, the mark on the flywheel aligns with the bended plate. Please look at the images to see what I mean:

imgur.com/a/g3Fz5kD

When flashing the ignition while running the engine, the mark on the flywheel does not align with the plate at idle. However it shifts somehow "digitally" when revving a little bit, but still not hitting the bended plate as a mark.
Can anyone explain how I should proceed to make sure my ignition timing is set correctly?

Thanks in advance!

Ahh btw, I bought an '76 YZ125 engine coming with an inner rotor ignition. I was checking if it would fit the MX, but saw one more red cable coming from the stator. The MX only has four cables: White/green, white/red, brown, black. The stator from the YZ has: White/green, white/red, black, brown, red. 
So would I need the CDI from the YZ too to make it work? 

How far are the marks off?  A whisker or 2 inches?  Firing early or late?

The early Hitachi CDI boxes don't age well.  Most don't work anymore.  Sometimes they start firing early or late quite a bit.  There might be an aftermarket CDI box made that could fix it if that's what yours is doing.

While we're on the topic of CDI boxes, yes, you will need the YZ CDI box that matches the YZ ignition.

First step for timing is to absolutely make sure the marks are aligning at 2.0mm BTDC.  (Or whatever you want timing to be).  This needs to be a precision measurement.

The marks should align using a timing light with the engine revved up a little.  If they are off a lot, something is probably wrong with the CDI pulsar or CDI Box.  If the marks are off only a little, could the timing pointer be bent?  

Yamaha manuals sometimes have mistakes.  That might be a "combined" manual that covers all the MX models?  They probably used a drawing for a 250 or something by mistake.    Here's the correct picture for your CDI timing from an MX175-specific manual.