Manual or power?  If power, what system are you using?  And if power what size/type booster are you running and does the system have a revised pedal ratio?  If you are running manual brakes with a stock ratio pedal, going to 1.25" will take you in the opposite direction if your braking is already inadequate (pedal effort increases with diameter).  From other posts, 15/16" may work better but this is a general recommendation that can't properly be answered until you provide full brake system details.  Also describe what type of distribution block/valve you are using and verify that you have the front and rear brakes properly plumbed to the correct positions on the master.

You have two opposite conditions - 1-1/4" will reduce brake travel but you would have to stand on it to stop and 15/16 will reduce brake effort but extend travel so there may be multiple problems.  Some pictures will help.  Are you using a dual reservoir master?  What front calipers are you using?  If using late 60's Mustang or Granada see the MustangSteve web site for the Granada conversion to ensure that you do not have the front calipers on the wrong side.  That usually causes a mushy feel but can also increase brake pedal travel as well.  What rear discs are you using and have they been properly set?  Some require multiple applications of the e-brake to get the pads properly positioned and reduce travel.  More details on all components front and back - including brackets, calipers, rotors, etc. are really needed.  Could be a mis-match of parts.  The stock distribution block on a 66 is not ideal for a dual master.  I'm sure you'll get a lot of suggestions here but the more details you provide, the better the responses.  Please also describe the specific master you are using, whether the pedal actuation pin is in the stock location and what M/C push rod you are using - straight, curved, etc.

Picture of front brake system. I also use stainles brake lines at all corners.

What pads did you order with your kit?  For the R-4 it says "Optimum R-4 operating temperatures are 450°F and above.  Throughout the entire heat range, the carbon kevlar material will give extremely consistent modulation and predictably smooth release characteristics up to threshold.  Not recommend for street use!" so if you are not getting them hot enough, you may not be getting proper action.  On the other hand, if the pads were not properly bedded (whether the R-4 or the R-4S) they won't want to stop if they are glazed.  Their web site states that 1" is optimal for the M/C.  The standard 66 distribution block does not have the safety features of the later blocks if your front or rear system fails.  Do some searches on combo valves/distribution blocks and look at various plumbing options.  I don't think that the 66 block is causing your current problems, however.  Is your proportioning valve fully open for testing purposes?  There were some threads a few weeks ago regarding open and closed positions so make sure it is fully open for your product.

How far from the firewall is your brake pedal when fully "up"?  Is there a spring on the brake pedal?  If the pedal is too close to the firewall at rest, this could affect your ratios and although you probably can't go over-center, you may be losing effective pedal travel if it is too close to the firewall.

You may need to contact SSBC on the proper setup of the e-brake on their system to ensure that you are not getting excessive brake pedal travel while filling the calipers.

Other standard things to check - make sure your brake lines do not go above the level of the M/C as this can trap air than can't be easily purged.

A check that may help would be to block the rear system fully and check actuation of just the front brakes and if necessary repeat by blocking the fronts (wouldn't recommend driving on only rears).  At this point I am at the limit of my suggestions and experience.

For my manual 4-wheel disc brake setup, the master cylinder I'm using is from a 94/95 Cobra SVT, 15/16" bore, as recommended by Baer (rear brake supplier).  Pedal travel is more than I'd like, but firm.  Pedal presssure is higher than I'd like, but not unmanageable for this street driver.  Some sort of power assist is in the plans for the future.
Hope this helps.