No heat in car and now when I apply the break the entire car shakes.

First, my 2003 explorer had the clicking noise when I turned on the heat. Replaced blend door actuator, thermostat, cleared heater core, and completely bypassed the switch with the vacuum line attatched. The vacuum doesnt work at all. The air blows but it is always cold. It is leaking around where the housing for the thermostat is and I have no idea what to do next. The vehicle will never reach operating temp on the gauge until after I have been driving for awhile. Recently the o/d off light has been flashing after about three to five minutes of driving. But the o/d is still on. Also, when I was coming off the interstate and applied the brakes, there was a loud knocking. Release the brakes and then a knock. But now, as soon as I apply the brakes, the entire car shakes violently and I got stuck on the way to work. Replaced rear brakes and rotors. When removing the rear left rotor found what was left of the parking brake sitting freely. Advanced said that I wouldnt need to purchase and install a new parking brake but now when I go to install the top bolt for the caliper the bolt goes in at an angle and will not tighten all the way. Also where the transmission meets the engine there is a leak. It has a red hint to it so im pretty sure it's just transmission fluid and not oil as well. When I start the vehicle now there is a loud high pitch squeal and then the sound of the lifters. This is my only ride to work and I cant afford to take it to the crooked shops around here.