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Unfortunately I don't have the greatest news. I was hoping someone would have told you this when you got the part to save the trouble. I usually tell my customer that when they change the cylinder out with the transponder to do it in the Ford parking lot. The reason is after you change the transponder, you change the frequency and the keys need to be programmed back to the vehicle.
There are locksmiths that can now come to you and do the programming at the vehicle. I suggest seeing if you have one in your area that can do this. If not, call some local shops to see if they have the Ford IDS scan tool with programming to try and avoid the dealer fees. Last resort is to tow to dealer for the programming.
The stage you are at now is you have to program the keys. I'm sure as you are trying to start, the theft light is flashing constantly while cranking. That will be the give away as well.
I wish my news was better for an easier solution, but there just isn't in this situation.
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