I'm looking into doing a front disc brake conversion on my '65 coupe. It has a C4 trans that I will eventually swap for a 5-speed. Keeping this in mind, I've been looking for a power disc brake conversion kit that will work with a manual trans but they all say "auto trans only."
Does anyone know of a power disc brake conversion that will work with a manual trans?
Also, is the reason that the power disc brake conversion kits out there will not work with a manual trans because the clutch linkage/cable will be in the way of the booster?  

I just completed a C4 to T5 swap and added power brakes when that was done. Scott Drake has conversions that are for two or four wheel disc brakes.  That is what I used. I also installed a Modern driveline cable clutch with the T5 and everything fit. If you have headers the clutch cable will be hasle ie finding headers that will miss the cable. If I were going to do this over I would go with the Hyd. clutch kit. And yes the "Auto only" is because most conversions get in the way of the clutch linkage, I had no problem with the cable clutch.
metropartsmarket.com is where I ordered the brake conversion.  

Yeah I agree with restomod. When I did mine I also used the cable clutch and it has limited my choices of power brake units because it comes out very close to the right of the old brake master cylinder(not the Modern driveline unit) and there is no room for a power unit. When you change over keep this in mind. You can go with one of several cable clutches on the market or you go with a hydraulic clutch. Look at how they are mounted because this affects mounting of a power brake unit. I agree, I would go with a hydraulic unit next time, but just be aware of the clearance issue when you buy either.  

You might check out Mustang Steve and see what he has to offer. Just google Mustang Steve.