So looks like you have 94-98 GT/V6 brakes front and rear, but running the stock MC and booster.
That pedal combo should be extremely soft, not hard like you are experiencing. Judging from the looks of the brakes, and lack of contact on that rear rotor, I would make a guess that one or more of the caliper pistons are seized and that's why the pedal is so hard.
It's not the correct MC/Booster combo anyway for the brake setup. You should be running a 94-95 GT 1 1/16" bore master cylinder and a 1993 Cobra booster. However, I think your brakes have other issues going on, and what I mean by that is seized calipers or slide pins or possibly no vacuum at all at the booster.
Engine off, pump the pedal until it's rock hard. Start the engine, and the pedal should sink once vacuum begins to pull from the booster. That braided vac line to the tree is interesting, but it probably is leak free. It's not uncommon for a MC to leak out the back into the booster and destroy the diaphragm giving you a huge leak.
I'm banking on seized calipers though. Jack the rear end up to get both wheels off the ground. STart engine and get the rear wheels spinning and lightly apply the brake. Can you stop the rear wheels easily?