I hope you find the lost keys.
Do you have AAA? If yes, they will cover the first $100 of the replacement cost for a locksmith to come out for an on-site replacement. Even if you don't have AAA, the best advice is still call around to local locksmiths and find one with a key programmer to come out to you. Most charge $100 to $150 to make and program 2 new PATS keys on site. It certainly is not a cheap fix, but really is the most viable option for dealing with this issue.
From there it gets more complicated. If you have already pulled the ignition cylinder you can get a replacement cylinder with 2 new PATS keys at Autozone and most other autoparts stores for around $50. You will still need to get someone with a key programmer to set up the computer. Chances are good you can talk a locksmith into doing the programing for around $50-75 so you might have save some $ versus having the locksmith make the keys from scratch. The headache is all your lock cylinders need to be rekeyed if you want it to match the ignition, or just pull one and have a matching non-PATS key made for the doors and rear hatch for cheap (like $10).
It is possible to do the computer programming yourself with the right equipment. Basically two choices on this. There are stand-alone $200 key programmers on ebay which perform the dealer functions to create new sets of PATS keys. They don't have any other functions besides making keys so locksmiths, repo guys, and car theives seem to be the only real market for these devices. If you really wanted to do this right on your own Ford does sell its IDS software license to the public for $600 per year which will not only make keys but also runs every other computer function, including the ability to reflash your system and customize some tuning functions. Keep in mind that you will still have the expense of buying the new keys with any of these options.
Other route is what Koda noted: pull key(s), ignition, locks, and PCM from same year and options explorer at a yard.