1. silicone caulk? did you just squeeze it in until it came out the other side? i get that tingling too sometimes.
2. your "bear trap" pegs are great, but i can see them interfering with your shifter. the one that i bought is longer and sticks farther forward, it made a difference with my boots.
3 without trading out your box for a shorter one ala pelican case, i'm not sure what you could do. that one you have is really high.
i sure enjoyed pt II and look forward to pt III!