Well it turns out that it wasn't my Transmission, or CV joints... The source of all the noise during braking was that one of my brake pads shot off the caliper and the piston on the caliper gorged itself into the rotor! What a mess, fortunatly I only have to spend $150 instead of ~$2000

'99 Mystique LS -Pale Green Metallic, grey leather int. -Infinity Kappa Speakers, Alpine head unit -Oooo I took off the badges in the back! -Ford "Fixed" dash... Student at the College for Creative Studies, Automotive Design