This really is beyond the scope of this thread. You should start a new thread.

Anyway...

Let me get a few things straight:
You start the car with the "yellow" key, and because the "green" key is close enough to the ignition, this allows the car to run?
Does the yellow key also manually unlock the driver's door?

If yes to both of those, then you can pop the metal key flange out of the green key fob and put the yellow metal key into the old green key fob. That will at least get rid of one problem.

Regardless of all of that, you cannot reprogram the security system in the ignition to accept the old keys. Also, you won't be able to program the wireless entry system to recognize the wireless lock/unlock signals from the fobs that match the new ignition. When you get a new key from Chrysler, it can be programmed to match the car's security system. But once a key is used in a car, it will not be accepted by another car/ignition.

Keep in mind that there are three separate security systems at work here.
1) the ignition security - involves the metal ring around where the key goes in the ignition and a small chip (pictured in my early posts in this thread)
2) the wireless door lock/unlock and alarm/panic system and the transmitter in the fob
3) the physical locks and metal keys

Each of these three systems needs to have its matching partner or it won't work. The key fob contains 3 of these partners - 1 for each set. You can swap them out between fobs, just be careful to keep them straight as to which is which. In a perfect world, you swap all three parts at once - thus keeping a working set together. Unfortunately, when your dad replaced the ignition cylinder, he broke the set of three that stay together.

If I had to guess, he replaced the ignition cylinder because it was locking the steering wheel and making it stiff or impossible to turn the key in the ignition. This is a very common problem. Your best bet - if you still have the old ignition cylinder would be to mod it so that the steering wheel locking pin is shaved off (search other threads for sticky ignition fix) and put the old ignition back in. Then all of your old keys will work properly.

In the case that you no longer have the old ignition, then you are properly screwed. You'll likely have to pay the dealer to reprogram it for you. Though, in actuality what they probably have to do is get you a new security module and set of keys from Mercedes. These things are designed not to be programmable as an anti-theft measure.