You did not mention it but I would think you heard a hissing noise coming from the underside of the dash behind your steering wheel area...either way I'd say you have the beginning of a vacuum (power)booster problem. It may be intermittent now but it's going for sure. The vacuum booster is what your master cylinder is mounted to...especially if there are no fluid leaks such as wheel cylinders, lines etc.

Check out the wiring to sensors for any damage, Try resetting light by disconnecting neg battery terminal clamp , remove, then replace and tighten.

One question - is the vibration noted mostly through the steering wheel? If yes, then several possibilities; warped brake rotors, worn front wheel bearing, worn / faulty strut or shock mounting - though if related to worn suspension bushings or shock mounts, this may be felt at different speeds and perhaps not just over 50 MPH.
If the vibration is felt through the chassis (such as drivers seat) then the most likely problem is the rear wheel brake rotors are warped - you'll feel the vibration (pulsing) as the brakes are applied.

First step is to further diagnose / inspect for the problem. Check the 'How-To-Guides' on the AutoMD website for how to inspect the front end and suspension for wear and excess play. There is also information in the 'How-To-Guides' about how to replace the brake rotors. Be sure to replace the wheel / bearing seal - if replacing the front rotors - as a set, and inspect / replace the wheel bearings as a set. The brake rotors are replaced in pairs.
Try the many on-line auto parts sources, such as; www.RockAuto.com or www.autopartswarehouse.com for the replacement parts.

Check out this write up it may be able to help you!

http://freecarsupport.com/.../...when-i-am-braking

Bad master cylinder, internal leaked at the primary or the secondary pistons.

brown fluid is a sure sign of contaminated fluid, completely flush sys and replace with fresh brake fluid.

Ususlly, this is the brake wear indicator - built into the disc brake pads. They have a small piece of metal that makes contact with the brake rotor when the brakes are not applied - to indicate time to change the disc brake pads; indicating thin friction material.
Try the 'How-To-Guides' feature on the AutoMD website for more specific detail to inspect the brake pads and rotors.
Try the many on-line auto parts sources, such as; www.RockAuto.com or www.autopartswarehouse.com for the replacement parts.

Absolutely not, you have to get the air out. I have a feeling your cause was not the master.

First of all did you bench bleed the master cylinder be for you installed it ? Thats where you put it in a vise .fill the resivore attach the hoses to the line outlets and put the hoses in the resivore held under the fluid and then using a screw driver and pump the piston till all the air is out of the master cylinder before mounting.

here isn't a whole lot left to try I wish I could drive it and feel the vibration that would help a lot but does the car make a lot of noise when it happens like possibly a droaning noise if you don't feel it in the steering wheel then we can probably rule out he steering rack, I see that axles were done and rotors and drums brakes but has anyone taken a good look at the wheel bearings Its kind of a long shot but it looks like just about everything else has been done the fact that it is speed related really makes me think about something with the wheels and may be if one of the wheel bearings is loose enough it might start vibrating

- Rick

The problem could be warped discs, have had this on my jeep (needs another set) and is a known problem.

if i am not mistaken, you would have to drop the fuel tank, to get to the rear dif. and there is a little c clamp that holds the axels in place. then you have to cut the old bearings out and press on the new ones. I did this on a 2000 Jeep grand Cherokee but on that there was no need to get into the rear diff, just undid all the brake hardware and attatched a slide hammer to pull the axel out. dont have a press so brought it to a local shop.