Well, just make sure you let the work air-cool. Definitely getting a lot of heat in the weld area, but that shouldn't be an issue as long as you don't make things brittle by quenching. 10 mm is very robust. I think everything is ok as is and adding additional gussets probably won't be of a lot of benefit. You could potentially add a bit of stiffness by doing so, but I doubt if you would detect any benefit when you ride it. Accurate fitment of the spacers in the front and good fitting fasteners all around will likely will prove more helpful. The rear mounts with the swing arm pivot incorporated into the back of the engine case is about as good as it gets. The weak "link" in fabrications like this is usually in the connection to the tubular portion. You have to have fairly frail brackets or mounts for them to give up before the connection to the frame. Look at any factory design and I think you will note that mounting anything including the engine, is accomplished with comparatively thin stamped sheet metal components. Heavily loaded mountings are often made in two thin pieces and weld to the two "sides" of any tube instead of the center. Single element brackets also attach to the side in most cases as well. This is because (depending on the direction of the load) doing so spreads the load out in a larger, friendlier area on the tube and reduces the likelihood of fatigue cracking in the tube. This is usually much more catastrophic than cracking the bracket, and consequently you see cracked brackets more often than cracked tubes due to this design preference. In your case, the rear mounts are very strong, and will feed all the loading into the original frame tubes. Unfortunately, the result is that there will be large forces at the ends of the plates where they meet the top of the tubes. This is the place where it is much better to have a bracket design that attaches to the side of the tube rather than the center, because the tube can "move" a lot more in this area when loaded in this direction which is easier on the material. Or in other words, the load is in effect spread over a larger area even if the weld is exactly the same size. So down the road you would be wise to keep a close eye on the tubes for cracking at the ends of those big mounting plates. This of course would be the likely location of trouble even if you did design the mounts for welding to the sides of the tubes as well, just less likely. Not trying to raise alarm here, just advising you keep an eye on these areas as the miles rack up. The good news is that steel is nearly universally used for good reason. All steels have a fatigue (aka endurance) limit. That means that if you don't load or cycle your load beyond a certain threshold, your design will last indefinitely. Exceed those values and your design can be relied on to fail in (hopefully) a predictable way. Materials with no endurance limit (like aluminum) will always eventually fail, no matter how kindly they are treated, so you have to be very careful to decide what an acceptable lifespan will be. Hopefully in your case, your design will be on the "good" side of the curve and you will live happily ever after - just keep an eye on things! This would be a good (I think I mentioned this previously) place to braze the joint. This is good because the fillets made with brazing will be much larger than welding and spread the load over a much larger area. Additionally, (with sufficient skill) the steel will be heated to a much lower temperature which will not disturb its original mechanical properties. You can braze with your tig torch, but as you are still getting acquainted with using it to weld, I suggest that you weld both sides of your plates, but do NOT weld the very ends. This will spare the tube from getting so much of a stress riser in the center, and move those loads into the end of two welds, one on each side.
Also, as a guess, maybe you are not using enough power when welding. This may be counter intuitive, but the logic is this: The quantity of heat you place into the material is a combination of energy and time. Too little energy takes too long to build up enough heat to start welding, so a much larger area is heated up very strongly. Turn up the amperage, and the weld area melts very quickly, allowing you to weld and keep moving the heat impacted area forward and allowing the just welded area to start cooling - net effect is less heat injected into the parts. Aside from the gas shield, that's the great value of tig welding - speed and less heat.
The shocks on the black RD are from Race Tech and built to order. I don't have any personal experience with YSS. Very highly recommend Race Tech if you want to upgrade down the road. They don't sell you what they have, they determine what you need and build it for you. Results are exactly what you would expect.