Is this a new master cylinder and front/rear brake buildup? 
What MC are you using? 
What front brakes do you have? 
Did you get the booster from me or somewhere else? 
Did the MC come from me? 
Have the rear drum brakes been properly adjusted? 
If the booster did not come from me, did you adjust the output shaft to fit the MC you are using? 
Did you modify the pedal assembly and pedal yourself or did I do it?

I always have more questions than answers, but if you can answer all those, I will be alot closer to helping you with a solution.

The power brake pedal does sit lower than the old manual brake pedal.  It is that way by design.  Once you get everything dialed in, the pedal travel requirement will be alot less, so there is no reason for the pedal to sit up as high as the old manual pedal did.  All power brake Mustangs, at least through 70, were that way from the factory.  The PB pedals always sit about 1" lower.

Location of the brake pedal pin is very important.  Since the pedal ratio is 4:1, if you are 1/8" off in pin location, the pedal will sit 1/2" lower than intended.  Same for the position of the flanges at the front of the pedal support.  Normally they get repositioned about 1/16" closer to the pedal than the stock location.  Other than that, there is nothing that will cause the pedal to sit lower in its static position.  By design, you want it about 3/4" to 1" lower than it was with manual brakes.

How long is "parked for a while" ?

To adjust the booster output shaft, you must hold the outside of the booster shaft with some vise-grips while turning the hex bolt head at the end of the shaft.  There are two different boosters supplied under the 54-74000 part number.  Only one of them has an adjustable shaft.  Years ago when I first started selling those boosters, they were all adjusted perfectly when I received them.  Now, they are all adjusted about 1/8" too short for some reason.  So, multiply that 1/8" by your pedal ratio and that is the amount the pedal will move down before it does anything.  So, if the pedal is sitting 1/2" lower than stock in static position, then has to move another 1/2" before the booster output shaft touches the master cylinder piston, you will have a pedal that is quite a bit lower than stock when the brakes are fully applied.  I am not saying that is the problem with yours, just giving an example of potential for problems if everything is not done a certain way.

Pulled the mc and as suspected the booster is not adjustable. I took mearements and it appears to me that the shaft to mc clearance is good. Like I said I've got good brakes so I guess a little pedal travel is something I'll just have to get used to.

I'm out of ideas. Everything points to the booster pin mc clearence but my mearsurements say its ok. I may just replace the booster when I can with one of yours. Not gonna happen for a while though so I'm gonna drive it as is.