As you mentioned, the dark marks are not necessarily indicative of stress. They are quite common in young dragons and I feel the name is misleading. They are often seen when they darken to bask and warm up.
I like how your tank looks and is configured - quite nice! I can help you fine tune the lighting to make sure everything is just right for your buddy. Is your ReptiSun the 24'' T8 bulb or the 22'' T5 with a 24'' fixture? One needs to be set closer to the basking area is all. I also suggest turning the fixture so it's shining downward over the basking area rather than outward. It will be much more effective this way. Can it be mounted to the top of your tank?
The 100w MegaRay is a nice bulb but has a narrow beam of UVB. It is most effective at about 10-12'' above the basking area. At this distance you may not get the right heat gradient across the tank which is important. Do you have an IR temp gun or a digital thermometer with a probe to accurately measure surface temps? Or are you relying on the dial thermometer on the back wall? The dials aren't very useful for measuring surface temps so I'd use an IR temp gun or a couple of digital thermometers with probes (one for the basking surface and one for the cool end). You want the basking zone to be between about 100-110 with a gradient down to about 75-80 or so on the cool side of the tank. You might need to play around with some different lighting configurations to achieve this. Think of it as two parts. One part is appropriate UVB exposure which is set by putting the UVB lights at a set distance based on their output. The other part is heat gradient which depends on basking light wattage, distance, and output (some can be dimmed).