Welcome to the forum! It may take a little while for Clyde to settle and that is pretty normal as you said. The dark lines are common with young dragons and often have more to do with them darkening to bask rather than stress related so I find the term stress marks to be misleading. Can you post some photos of Clyde and his setup? You can upload photos here
https://www.beardeddragon.org/useruploads/ and post them to your thread using the XIMG button when you reply.
Unfortunately the kits don't come with great stuff and some items can wind up being harmful. Some of them come with sand which shouldn't be used. Instead, using a solid substrate that is easy to clean such as non adhesive shelf liner is a better way to go. The lighting is also usually inadequate. It's critical to invest in a high quality
UVB light. Using a T5 tube is probably your best bet. Is this a 40g kit or a 20g kit? The size (distance from the bulb to the basking area) makes a difference regarding which bulb to use.
Another issue with the kits is that they don't usually include a good thermometer. You want to use an infrared temp gun or a couple of digital thermometers with probes to get accurate surface temperature readings. You can then adjust the basking light by changing height or using a different wattage in order to achieve proper temperature gradients. You want the basking surface to be around 100-110 or so. There should be a gradient down to about 75-85 or so on the cool side.
It's good that you got rid of the red bulb. The CHE might wind up being helpful on cold nights but if the temperature in the tank stays above 65 or so overnight then you don't need any additional heat. A cool down overnight is normal for them. Even in the winter when my house goes colder than that, I use just enough power in a CHE to bump the temps up to about 70-73 or so.