You said all turn signals work but not the brake lights. That sounds like a very easy problem to fix. It means bulbs are all good, flasher is good and T/S switch is routing signal pretty good. Grounds are good.
Typically you will have 7 wires in and out of the T/S switch:
1. From brake switch output
2. To RF brake/turn filament
3. To LF brake/turn filament
4. To RR brake/turn filament
5. To LR brake/turn filament
6. From flasher La vintage vehicle to
7. From flasher P
This is the list for older aftermarket clamp-on switches without 4 way and with P, L and X flasher terminals. Variations will apply. As well as the 8th BLK wire for horn. You don't need to use it , you can wire the horn separate if that is better for a 1949/50. All part of adapting a modern pre wired universal harness to a vintage vehicle.
As you know the running/parking lights front and rear are on a different bulb filament and are controlled by the headlight switch. You need dual filament bulbs.
There is a mistake on the list of pinouts in the instructions. Anyway, be sure you have the Speedway wires plugging into the appropriate wire/function on the T/S switch that they call for. Don't rely on old T/S switch wire colors.
14A & B H Light Blue Left Front Turn Feeds the left front turn lamp bulb high filament and the
right 
left turn dash indicator lamp