OK Christian,
You're ready to go now.

Obviously, you need the two tiny screws to the motor/motor mount.
Please note that the Right side with the universal joint, the gearbox is INSULATED. You can tell by those little plastic collars that are around the screws. Never over-torque the screws- the collars will break.
So I call one gearbox the "hot" side, and one the insulated side.
The gearbox on the left is charged hot.
And so is the main frame.
And so is the motor frame.
And so is the motor shaft.
And so is the shell.
So the right gearbox must be insulated from the frame.
And the right wormshaft must be insulated from the motor shaft.
Now, some K&S brass tubing will work as a U-joint connector to replace the stock one. I don't remember which size.
And you might want to do that just to get it running.
The u-joint cups have a hole in them- which means if you push them too far down the shaft, the shaft will protrude into the hollow area. You don't want this since each shaft is charged and you will get a short. As I look at yours, one of them is pushed too far onto the shaft because they are too far away from each other.
Super Important!!!!!! Do NOT solder on that tab at the right gearbox as is.If you solder on that tab while it is in place, you will melt the plastic insulator-- they are very fragile. What you must do is remove the solder tab by removing the screw and THEN solder a jumper wire to the tab.
So the motor gets juice from the jumper on the insulated side, and from the frame on the hot side.
Now, I have already suggested using Atlas parts as replacements/improvements (page 2 of this thread).
The SD7/9 CHINA! flywheels are GREAT for kitbashing because they have a plastic insert so that you can hand-press them onto the shafts. Newer flywheels are machine pressed on and require a puller to move.
The u-joint is two Atlas parts (last time I ordered, I thought they came together and was disappointed). They don't have photos for such old parts they will not make again.
This is from my Trainmaster. Same orientation as in your first shot.
Now, on the hot gearbox, your screws are obviously missing. You can get new ones from your donor.
However, even though the screws connect the juice from the gearbox down to the main frame, you still need insulators between the gearbox and the frame-- they are probably missing. They are clear rectangular acetate. The reason is that you want BOTH gearboxes at the same height. Admittedly, we are not talking about much, but I would do it.
Now, to get this thing to run. Problem is that the wheels can bounce around and touch the frame right above them. You will probably see semi-circular marks on the frame where the wheels are rubbing. Some wheels won't matter since they will be charged hot the same as the frame. But if opposites touch- short!
Solution- take a piece of clear packing take and cover the entire area from the fuel tank outward to the edge (both ends). Then take a Xacto knife and trim the tape away from the gearbox holes and from the frame. Now, you have insulated the frame from the wheels.
Second- the truck side frames are micro-meters from the side sill when assembled. The hot end is no problem, but the insulated end will cause a short.

Solution- jack up the shell just a little bit. I use a few of those hundred Micro-Trains black plastic washers that come with truck packages that I have in my junk box. You have to trim them a little, but I superglue them on the top side of the frame over each screw hole. Now, the trucks don't touch the side sill.

If you do these things, you should have a pretty good running loco when finished.
I do a few more things, but these are the really important ones.
Ron Bearden