Here's what I think has happened. The MC went out, (I would feel more sure of this if you said that there was fluid on the booster end of the MC when you removed it.) At that point you began bleeding using your wife as assistant and the engine NOT running. This means that you had very little pressure at the wheels when bleeding, so you ended up with air.

You THEN replaced the MC, but could never get it properly bled because again you bled with engine not running. Engine running will give you the pressure you need due to the booster helping things along. Some power brake cars require this and some you can get by without the boost. If you have a 300 pound weight lifter on the pedal, then you could probably get by without running the engine.

If you have indeed been bleeding with engine not running, you will need to start the engine and roll down the windows so that your wife and yourself can communicate over the engine noise and then bleed.

I've been there, done that with this whole scenario.

Good luck and Merry Christmas,