Good video. A couple things:

1. The seat heater foam cut away pretty much stinks as you mentioned. I couldn't figure out an easier way!
2. The odd shaped carpet pieces you asked about - you need to wait until the body is installed and you install the aluminum pieces that go between the door opening on the frame and the body. They cover that area.
3. I went to Home Depot and got gray indoor/outdoor carpet for my trunk. Thinner than what you used, cheap and easy to install. Worked great. Pics in my build thread. Index in post 1 should tell you were to look if you are interested.