Much better pictures. I didn't realize the shock location had such an offset. Since you are not that far along, I think I would redesign the upper shock mount a bit. But first things first. You need to determine the range of motion for the swing arm in order to decide on the proper upper shock mount location. Without getting into a broad kinematic discussion about these types of linkages, the primary goal of the original design is to provide a mechanical rising rate of motion to the spring and shock. The idea behind this is to have a softer and more compliant action for small deflections, but ever increasing shock/spring effort with larger and larger deflections. That way when you hit tiny bumps, the suspension easily gives way, but when larger ones are encountered, the suspension is not overwhelmed and bottoms out. This effect is provided by the large change in angle between the various linkage components as the suspension travels through its range of motion. For simplicity let us focus on the angle between the bellcrank and the shock. See the first picture. As you can see, your current angle is close to 90 degrees already, and as the suspension compresses, it will come up to and then pass 90 degrees. As it passes 90 degrees, the suspension will become softer and softer - exactly the opposite of what is needed. You need to remove the spring from the shock so you can move the suspension through its complete range of motion.
Unfortunately you have removed the original suspension and no longer know what the original top out and bottom out angles for the original swing arm were, so you will now have to estimate those positions and work from there. Don't underestimate how very important this is to do. Take the shock off and put a block under the swingarm to locate its lowest position, and then lift it up to its highest position and measure. Fixture the frame and blocking so this can be repeated over and over reliably without changing. Then you can put the shock back in (without spring) and see where you need to go. Obviously you want the shock to be fully compressed and fully extended with the arm at each end of its travel, but there is rather more to it which is where that bellcrank angle comes into play.
For your linkage, you will want the the angle between the bellcrank and shock to be at 90 degrees when the suspension is fully compressed. At 90 degrees, the shock has the greatest mechanical advantage over the linkage, and therefore resists further compression with the greatest force. As the suspension is relaxed, the angle of the bellcrank becomes more and more acute, and the linkage has more leverage against the shock which has the effect of making the shock easier to compress. This is what you are after. At normal ride height with the suspension 2/3 or so uncompressed, small bumps will easily compress the shock and spring because the linkage has a lot of mechanical advantage over it. As the suspension travels farther and farther and that angle gets closer and closer to 90 degrees, the mechanical advantage gets lower and lower making it ever more difficult to keep compressing the shock.
Once you figure your swing arm displacement, you can adjust the bellcrank to have the right orientation to the shock (to get that 90 degrees at full compression) by adjusting the length of the lower link and the upper shock mount location. Yes, this is a pain to do as there you pretty much need to change everything at once and subtle changes have rather a big effect. The good news is that you have everything mocked up so you have a starting point to help you determine where you need to go.
To illustrate, let us assume that your swing arm displacement is currently perfect where it is. You would want to take the spring off, and put the shock back on. With the suspension in its lowest fully uncompressed position, look at the bellcrank and lower link. You want the angle there to be 90 degrees. See picture 2. Then raise the swing arm to its max upward travel position and fully compress the shock. You will see that the bellcrank to lower link angle has become much larger than 90 degrees. The larger this angle becomes, the stiffer the suspension will be, so moving the links mounting point and changing its length will have a profound effect on the suspensions behavior. Now you can determine the upper shock mount location. Fully compressed, you want the shock to bellcrank angle to be 90 degrees.
Be advised that this is just a starting point, and that the behavior of the system is affected potentially dramatically by seemingly very tiny changes in any of the components or their mounting locations. But this should get you fairly close. And yes, this is a very fussy and time consuming process and likely you will have to mock everything up several times to get it right, but I am not sure how else you can proceed unless you can acquire an original bike to simply measure and copy exactly - which is not all that easy either.
As far as the structure goes, I don't think you need any extra shock mount tubes, but since I am sure you need to move the location, I suggest some different tubes. See pic 3 and 4. I would replace the tubes you have and angle them to meet the intersections of the existing cross and side tubes. A bit trickier to make, but not as bad as you might think. The way to do it is to get your shock positioned in the right place and clamp it here with something and bolt the upper fixture into it. Then just cut and try each of the four tubes one at a time. Once you have them all fitted up you can tack them in place and unclamp the shock and check the action by moving the swingarm through its travel.
As far as the side bracing goes, I would simply add one on each side similar to the original factory tubes. The strongest arrangement is in red, but you can alter the location rearward if you want a particular look or not obscure the shock from view.