I have original 4 into 4 exhausts, but apart from that I currently have almost the same set up as yours:
Interesting that you ended up with #35/#105 jets on the stock intake and 4-4 exhaust system. Was #40/#100 the original jetting for your bike as well?
I have the little rubber spoiler on the front of the air cleaner box and the original tool tray.
I have both as well. Well, I did until last night. I just installed a NOS K&N air filter last night. It is a single oval filter and mounting plate that mounts to the inlet of the stock plastic manifold. In other words, it takes the place of the stock air filter box.
I admire how you've done yours in what I believe is the correct order -float levels, -mains, -needle clips, -pilot circuit, I wish I'd had a similarly sensible approach when doing mine.
I was trying to follow advice I had read on the forum - I believe I had read a post from TwoTired that recommended that order. However, I didn't entirely stick to it because mine was running excessively rich over most of the throttle range with my initial carb config. So I did deviate from the order a bit to get it a little easier to ride earlier in the process:
-float levels, -first pass air screw adjustment, -needle pos, -main jet, -pilot jet / air screws
Mine currently has good plug color, starts easily and runs well in most situations, however when cruising in top gear at highway speed if I close and re-open the throttle I get momentary hesitation.
I was experiencing a different symptom in what might have been the same condition. When riding on rural highways in hilly areas, I think I sometimes created a similar situation near the bottom of bigger hills. Increasingly closing the throttle as I descend a hill, sometimes completely closed by the bottom on the bigger ones, and then transition back to opening the throttle. And at that point when I just started re-opening the throttle, I would sometimes experience what I think was a slight missing. I was still on my pilot tuning journey when things were still too rich but closing in on where I am now. I did not experience that symptom with clean plugs… it would develop that symptom after riding a while. I think the issue was that the plugs were getting lightly fouled during highway cruising... perhaps enough to get away with under less challenging cylinder conditions... but not in conditions such as that. I suspect that based on how the plugs looked after riding in that scenario, that the symptom developed / got worse with more highway riding, and that it went away as I leaned out the pilot circuit.
I wonder if your symptom might be that your pilot circuit is on the other side of ideal (a little too lean vs a little too rich). I don’t know… just speculating and guessing based on my experience with mine. I don't have much experience on the other side of ideal in the pilot circuit yet (lean vs rich).