Sounds to me like you have air in the line.  Specifically, the master cylinder.  Bleeding one can be very frustrating, and most on this site have had the same problem.  It took me a couple of months to get mine air-free. 

Everyone has his/her own way of bleeding.  I started by bench bleeding the MC.  Then the rest of the system using the gravity method (fill the mc leaving the top off, then opening each brake bleeder screw till the air bubbles are gone.) doing it several times to make sure.

Have a good time at it:-).  We all feel for you.

M1M, I understand the frustration, and echo lowercasesteve's comments about trouble getting a system air free.  I have manual brakes on my 65, and replaced m/c, lines, hoses, calipers, rear cylinders, and combi prop valve last summer.  I worked on trying to get it bled to get a firm pedal for almost 2 weeks, and was tempted to drive it off a cliff, on more than one occasion.  I eventually caved, and took it to my mechanic for my daily drivers, and he put his pressure bleeder on it, and fixed it.  Hornman put his plans for making your own pressure bleeder in the "tips & how to" section of the forums. I have no experience with Mustang boosters.

I bench bleed a master by using two short lengths of tuning I made up to basically loop up from the ports and into the reservoir.  I use whatever adapter I need to make those lines fit the particular master I'm bleeding.  Then you take a Philips head screwdriver and use it to move the master cylinder piston inward and allow it to spring back outward.  You do that until your arms feel like they are going to fall off.  Then continue to do it until there are no air bubbles coming out of the tubes.  It can take a long time, and the issue I'll bet you are having is that the fluid got aerated and it seemed like no air was coming out, so you figured you were good to go.

Once the master is bench bled, install it and bleed the brakes.  I use a length of clear 3/16" vinyl tubing from the bleeder nipple to a clear container (water bottle, Gatorade jug, etc.) which I put enough clean brake fluid in to cover the end of the tubing.  Then pump about 20-30 times and check the line and container.  This allows you to literally see the air coming out and the condition of the fluid.  I go until I get nice clean, air free fluid, then move to the next closest wheel to the MC.  This method has always worked, where others have failed.  I always get a nice firm pedal this way, even on vehicles that are notoriously difficult to bleed. 

Finally, I'm sure you already know this, but make sure the bleeder screws on the calipers are on top.  The bleeders have to be at the high point or they don't work. 

Ohhhhh Gotchya....I see Lowercase, I assumed the the bubbles would surface but not the fluid.....

One question though, will this help remove the potential air in the MC also?  or just the rest of the system....

Thank you TKO, If these fail I will be starting over and doing exactly as you had said (mind you when I bleed I do the hose to bottle thing also, I prefer that over all other methods)

I know at one time somebody mentioned that you can put the calipers on upside down where the bleeder screws were on the bottom.  The air trapped stays at the top of the caliper.  This was on Granada calipers but it is worth a check.

Alright MachRon and GPat. thank you both also!

-Pat I eliminated the factory Prop.Valve several years back in an attempt to rectify this very issue; this is when I put the Adjustable Prob. Valve in.

-MachRon I know this is going to sound Very Stupid but to remove the MC now is going to be a decent size SOB...I have the Borgeson Steering box with Power Lines running in the way, the front suspension connectors that runs from end to end, CLutch Lines....I mean Obviously I will, but if the PRESSURE BlEEDING can do the entire system, I'd prefer to avoid removing the MC.

UPDATE :
-See if this makes sense and if Im on any sort of Track Here;

When the Pedal is depressed with the car off (bleeding), the first 1" (possibly more) is all booster travel.  Next you can here a slight "click" which Im assuming is the booster pin hitting the MC cylinder.  Im determining this while watching the MC bowels blimp or wave the fluid within it.
Am I wrong to think the Booster Pin is to far in? should it not engage sooner?
 

I use same bleed method as TKO.  Works every time.
You can bench bleed a mc on the car. Just disconnect the lines from it and install some temporary lines from the ports to the bowls, below fluid level.  Use pedal instead of screwdriver to accomplish the same thing. When you get no more bubbles bend the temp lines to vertical above fluid level. Install the lid. That creates a vacuum to keep fluid from escaping as you reinstall the brake lines.

Then bleed as TKO described.

Also, you need to be sure the rear brakes are adjusted as tight as practical and that the self-adjusters are in good working order. If the rear brakes have too much travel, you can get symptoms where you press on the pedal and not much happens until the front brakes get full pressure and then whamo, you get full brake actuation all of a sudden when all four hit at once.

Rotor runout or loose bearings can also cause excessive brake travel.

Using a power booster with a manual brake pedal can cause a mushy brake pedal and sudden high pressure brake actuation.

A defective internal booster valve can cause sudden brake actuation after excessive pedal travel.

Brake lines running higher than the fluid level of the mc will trap air. Ditto with hard lines that have upward runs.  You want them flowing downhill as much as possible to avoid air entrapment.

My first efforts would be spent bench bleeding the mc, adjusting the rear brakes, then bleeding the system.

If you immediately go out and try a panic stop to try out your new brakes, chances are high you destroyed the pads. You must break them in gently with progressively hotter stops over many miles. If this describes your test method, replace thr pads. My experience has been that any pads with a lifetime warranty will not stop as well as cheaper or a peformance type pad.

I pretty much have the same setup as you on my 69.  I have the power Brakes with the Granda's brakes on the front.  I bought all my parts this winter from MustangSteve and it works really well now.  I bought the booster and pedal setup and had the roller bearing installed in the pedal support.  Id bet your pedal is part of the problem too.  You should have  power brake pedal for a Mustang.  
Steve69 

Thanks RED351.....you sound like youre on to something!.....but how do I correct the Rear Brakes from expanding prematurely, or, "braking that strongly before the fronts are activated?"

-are my shoes too far out? (there is no Drag on the rear, front yes)
-is it possible the Rear Cylinders are Seized?
-are they not getting enough fliud, or too much?
-are the shoes on incorrectly? (left and rights mixed up)

It has been 10yrs since I serviced the Rear Drums so I can not Recall what size they are, but Im assuming OEM Stock 69 Mustang; 9";  28 spline Drum Brakes

Hey Markin,

Yes it is am Adjustable Prop. Valve with the Knob on top....Plumbed out of the Rear Bowel of the MC straight to the Rear Line....

Most Current Update:
-I did my Third Run today (lightly driving to break in Pads) and this last time I stopped and turned the Valve all the up (I believe up cause it seemed to get easier to turn).  The Pedal Felt firmer to press, although breaking the vehicle seemed more difficult.  But that last point doesnt have much to compare to so I will have more info tomorrow. 
Def noticed a firmer pedal though......

unfortunately achieving a photo is nearely impossible...the area is too tight and full of lines, wires and crapolla

Patience and a BFH are your best friends when working on seized up brakes. An old timer (now I am one) showed me how to get things apart on my old Fiat once. First loosen the spindle nut so you have slop in the bearings then use hard wood block and hammer on front and back of the drum to get the frozen shoes to retract. I've had it work on the back too, but takes a lot more of the patience. I was able to save an unobtainium brake drum that way.

typically, the larger bowl is for the disc brakes in the front, and the smaller bowl is for the drum brakes in the rear.
Sounds like we found your problem..

M1Mustang69 wrote:

So ita confirmed, my Front Brakes are connected to the Port closest to the Rad and the Rear brakes are connected to the Port closest to the firewall.

This is Incorrect yes?

Mine has second Port Larger than first one and second bowel is smaller!