I think that is just shiny metal, but to be sure, NEVER EVER use teflon tape on brake lines. The threads are only holders. the seal is at the matching flares.
I think I would pull and bend those lower lines into place, unless they are too short. My luck, they would be 1/2" too short.
As far as the lines from the MC to the block, push/pull, tweek and force it a little. Starting the thread straigh is paramount, if the tube is a bit crooked, it will flex into place. It's just the way it is. X2 on plugging the upper hole. The "T" at the frame will do exactly the same thing.