OK - I might have something for you to check. When I put mine back together, I went with all-new factory-style everything (OEM replacement), to include new brake lines, calipers, master cylinder, distribution block, etc. - literally "everything" except the booster, since I ran into issues trying to get an OEM-style new one or mine rebuilt. I got it all back together, bled, and I could not get my pedal to firm up - couldn't figure it out... chased my tail for about a year after I got the car running - after several pumps, it would hold, but not good enough for driving.
After I received the booster and installed it, the problems still persisted - so 'that' wasn't it.
I did some more research, bugged the guys here, and thought about trying a bunch of different things... and then the light bulb went on for me when I was under the car - I'd installed the calipers on the wrong sides (passenger on driver, drive on passenger). Crap! Once I swapped them back to their correct sides and bled the system again, it was all golden... finally. The way I determined it was noticing that the bleeder valve was lower than the brake line inlet. Duh... felt like an idiot afterward.
I don't know if that might be your issue, but it wouldn't hurt to check just in case. (although, you did say the brakes worked fine before the engine swap and you didn't change the calipers)
Have you checked your power brake distribution block? I understand that if the proportioning valve gets 'tripped,' it won't work right until it's 'reset,' which I ain't gonna lie - I'm not entirely sure what that means.
Do you have your brake booster vacuum line system hooked up to the base of the carb, or straight to the intake manifold inlet toward the rear of the engine? I put an elbow on mine and went straight off the intake manifold. My 351C-2V has a pretty healthy cam in it (CompCams Magnum 270HR - 270/270, .566" lift, 110 degree lobes - 215/215 @ .050") - haven't experienced any vacuum issues.
Sorry if I've thrown out things that you've already checked - these are the things I've run into with mine.
Hope it helps.