The red silicone will blacken soon enough on it's own, or after it cures give it a shot of the black high temp paint.
As long as you can manage the heat without sealing the firebox door, you are ok with a gap. It just makes it a bit trickier to adjust the damper, especially in breezy weather. It will take several cooks to learn where the smoker wants to run with the least amount of fuss in fire management, but as a rule, most stick burners like to run hotter than electric or gas smokers. This is not as huge of a deal as it seems. Mine like to run at about 280° give or take a few degrees and the food comes out just fine. I'm an impatient feller anyway, so the hour or two shaved off a brisket cook suits me just fine and I can't tell any difference in flavor or texture from one that was cooked at 225°
If you burn charcoal only, you are missing some of the great wood smoke flavor.
Can't wait to see some food in that beast!