Are all the parts used or did you install a new master cylinder?  I would check the following:

1. With the spindle change, etc., is there a chance that the front calipers are forced to one side so that the piston is effectively bottomed and it can't move? Check to see that the rotors are centered within the caliper and the caliper is free to move over its normal range.

2. Are the pads you are using correct for your combination?

3. I don't know my years well enough but is your proportioning valve offset to one side?  If it is the type that must be centered to provide flow to front and rear you it may have shifted during bleeding - giving you flow when bleeders are open but perhaps not correct flow when the system is closed.

4. Not knowing how the pedal and booster fits between a Cougar and Mustang, is your brake pedal pulling fully away from the booster?  If not perhaps the booster is not operating properly (no boost) because it is not allowing a vacuum to be pulled and fully "charge" it.  You probabaly wouldn't notice this when bleeding but with no boost and the larger bore master you will fight to get any binding at the calipers.

5.  Related to 4, is there a proper gap between the actuator and the master cylinder piston.  This usually results in a system that won't release the brakes once applied but it is worthwhile to check.

6.  If you re-used the old master from the Cougar, how long did it sit?  Had it fully drained?  Did you attempt to bench-bleed it?  Are you sure that they master that was in the Cougar is the correct master in the first place?

That's where I would start until someone posts the real answer.

 

I can almost guarantee I know what is wrong with it.  When you installed the booster, did you enlarge the center hole in the firewall sufficiently so the rubber bellows on the booster do not touch the firewall at all?  Go to my FAQ page about boosters and brake pedals.  Near the bottom, there is a FORD template they used when retrofitting a booster onto a non-power brake car. 

The problem is the hole is too small and the sides and bottom of the hole grab the rubber boot on the booster and dig into the plastic piston keeping it from moving.  Of course, this will require removal of the booster in order to fix it, but you should be well-versed at doing that by now.

is it necessary to pull the pedal bracket also or is it not needed.i will be pulling it apart tommorrow.

wow! steve you were exactly right.dont even want to tell you how long i have been dealing with this.power brakes almost put me through the windshield the first time i hit them at mid speed.thank you  very much for the great advice. now the issue i have is its still hard pedal at idle and low speed.im pretty sure this has to do with vaccum and the big cam my 400 horse smallblock is putting out.tryed a vaccum cannister but it didnt seem to help to much.guess i need to talk to the hot rod guys to resolve this vaccum issue,unless you have a idea.  again thanks for the great advice,worked like a charm,cant belive how long i went with them that way and couldnt figure out how to fix them.  thank you.

A canister that is properly connected should work with 12 inches vacuum.  If you want a pump, the Ford diesel pickups used one that works well.  Still suggest using a canister with that.

my car has a check valve in the top of the booster.and i do have a cannister hooked to it also. i could always change the check valve if i can find one . just to be sure. already changed everything else.