Does the vehicle start? If not you'll have to re program the keys . You'll need a minimum of  2 programmable keys. Which you'll be able to do through the tool. But I'm pretty sure you may have to pay a subscription to used the fmp software in order to write the vin. You won't be able to do it on the tool, you'll have to use a pc/laptop. 

 If the tool does have a programmable module installation option available in special functions it is something that has to be accessed  while the old PCM is still hooked up so it can pull the necessary information out of the original to transfer to the replacement one.

  Get the key code by VIN from the dealer and write it down and have them cut you a cheap non  PATS key first to make sure key code cut  matches the cut on the one existing key. Next have them cut a fresh key from the key code with the proper PATS key blank (NOT MAKE YOU A CLONE KEY) After you program the 2 keys you should order a couple PATS blanks from Amazon and have a local locksmith cut them and you can add the additional keys yourself if you have 2 programmed ones with you.

usually you can bring the key you have to a locksmith, they should have chipped blank keys. maybe around $50 or so for just the key + cutting. then you should be able to program both keys that way. ive had a customer who only had 1 key available and needed me to program his blank pcm. he went to the local locksmith/ace hardware, to get another chipped key cut. worked out fine.  i had to perform a parameter reset. lmk how goes. 

 I find that the C@ck S@cking locksmiths now a days in my area just seem to just want to cut and clone keys now instead of stocking  a wide a selection of the proper PATS key blanks to cut and let someone else do the programming. If you need to  have 2 unique PATS keys and one of the 2 provided by the customer is a clone of the other one , it is going to cause you to have a very bad day. 

 i feel you man, some places wont even cut a key you bought from amazon/anywhere else. i went to ace to have them cut a key the customer provided me,  they say they couldnt do it. so i paid $100 for their "chipped key" . they cut their key but when i went to program it, it wasnt an eligible pats key. i ended up having to go to lowes and thank god the key cutter was a new hire and didnt know any better. he cut the customer supplied ford blank key for me. smh.  Ford needs to change this, if a customer loses a key and needs spare key, we cant do it unless we jump through hoops/wait on a key/ go to the dealership. but who needs an extra spare key  if a customer already has 2 keys. just my thought. i understand the security issues. i guess we just learn to deal with it. 

Can key programming be done with an ms906? It gives me the option but the one time I tried, it failed.