What would the transmission have to do with the power booster?(unless you plan on using a booster that is such a large diameter that it affects the manual transmission Z-bar setup)
Anyway...please do not this. A power booster does NOT improve braking...all it does is reduce pedal effort(assuming that it works correctly). Considering that the Mustang is a light car...power brakes are simply not needed. Back when they were sold no one had issues driving them with manual brakes to the point that very few chose the power booster option for 65-66 if it didn't come with the package they bought. Most of the people who buy an aftermarket power booster kit have trouble with them not working correctly...common complaints are increased pedal travel etc...the reason for this is that most aftermarket companies do not seem to have the correct pedal ratio required...their bell crank setup simply does not have the correct geometry to achieve the right pedal ratio. If you absolutely MUST have power brakes, my suggestion is to find an OEM power brake booster/linkage/bell crank setup and have it rebuilt. That way you can be ensured that the geometry is correct and avoid the pitfall that most people who user the aftermarket setups fall into. If a rebuilt stock setup is not an option and you must go aftermarket...I suggest the Mustang Steve setup. From everything I have heard, his power brake kit actually works correctly(no personal experience with it myself) and has correct geometry...but he uses a modified pedal hanger assembly to be able to use his booster and MC.
There is no issue with the dual MC and disc brake portion of your upgrade(even if you won't see a whole lot of difference over well maintained drum brakes except in increased resistance to brake fade and better performance in the rain) with most of the kits out there.
As for me...I actually want better PERFORMING brakes. SO I am going with the SoT front brake kit:
This maximum performance system is a must for serious street machines and high horsepower track cars. Offering maximum performance this system is a must for serious street machines and high horsepower track cars. Utilizing a deeper hat offset this system is a direct bolt on to '65-73 Mustang...
streetortrack.com
Which is one of the few kits that you can find independent information on how it actually performs(numerically) after the install:
We install and test before and after effects of Street or Track’s brake upgrade for early Mustangs
www.motortrend.com
They essentially got a 33% reduced 60-0 over the OEM-style disc brakes(and much reduced fading) which is an impressive real upgrade that you can quantify....and still no power booster.
Of course....to be able to use that particular kit you need 17" wheels to clear the calipers...but that is something I have no problem with. I wouldn't bother buying a kit that you can't find any information on test result numbers myself though. Disc brakes sure look pretty...but in 95% of daily driving they don't make any difference....if you just want disc brakes for slightly better braking and dont care so much about performance...the stock Kelsey-Hayes style setup with more aggressive brake pads generally has good results.