1996 Honda Civic My Honda Civic 2 door EX shakes when break

Please read all of this before jumping to conclusions. This Honda shakes fairly violently when breaking (sometimes worse than others). You can feel it in the steering wheel, breaks, chassis, all over but mostly in the breaks and steering wheel. My first thought was rotors so I changed them (no fix). Second thought was stuck calipers so I changed them (no fix), Third was CV joints so I changed both front axels (no fix), I narrowed it down to the front passengers side wheel area by lifting the wheels and checking each individually. The problem is definitely in the front passengers wheel area. I changed the Wheel bearing on that wheel (no fix). All the bushing are in good shape. WTF? Could there be a problem with the transmission. Maybe a bad transmission bearing? Outside of breaking the car runs smooth. Help!

One more thing. When putting the car in reverse the shifter barely makes it to reverse before "clicking" in. We have always just dealt with it. I don't know if this has anything to do with the problem or not.