I assume you got the correct brake pedal when you got the parts? If not, start there. I also assume you are not leaking fluid anywhere, otherwise find it and fix it, and the problem is likely solved.
To check the booster, start the car and let it run. Check to make sure you have vacuum at the booster with engine running. You should be able to tell right away, and the car may even die, as this is such a large vacuum line. Hook er back up and let it run long enough to build vauum back up in the booster. Turn off car, then slowly press brake pedal a few times. It should be fairly easy to depress for the first few times, then get harder as you deplete the vacuum reserve. If is hard right away, your booster is gone. Another way to check is pull the check valve/vacuum line off the booster after the car has sat for awhile. You should hear/feel air rush out of the booster, indicating that it is building/holding pressure.
The master cylinder would give you an erractically spongy or hard pedal without notice. If you are pushing the pedal while braking and it all of a sudden drops, or is unusually hard, your master cylinder could be bad. There are other symptoms as well. I did my conversion with junkyard parts, but bought a remaned master cylinder for it. I don't trust a junk yard cylinder, since you don't know what is in there. If the lid was left open at the yard, you likely had moisture in there that ruined the seals. If your booster checks out, I would put on a new or remaned master cylinder, just on the priniciple of the matter, but it will likely help your problem anyway. Another possibility is the combination valve under the driverside frame rail. I think there was a recall on these, but I don't know what the issue is.
If you have access to a lift (or jack stands or something suitable-don't use cynder blocks), you might put the car on a lift and get it up to speed, then have someone watch while you lightly hit the brakes. All 4 wheels should slow/stop at about the same rate. If not, you should be able to determine if one is not applying, or if one (or more) are hanging up.
Hope this helps. Good luck.