I came up with a cleaver idea. After poking around on the internet a little, I found some 30 pin connectors that are easiser to solder than the one that I was origonaly going to use, we can just use that to get the uC to interface directly with the iPod. I think that will be a lot easier and less expensive.
Just to give you some pointers on the specs of my uC, like I said it's a DS2250-32-16. It does not have an RTC installed in it, however I do have an RTC that could work with it, the DS12F887 (I'm not sure about the F digit but I do know that I'm right about the rest of the numbers). That RTC would be kind of good for something like this because it also has EEPROM built into it.
These are some questions for audioguru.
Can your FM transmiter be made with a 12V input?
Are the 2 variable cappacitors the same cappacitor?
Can I substitute the Vreg with an average 5V regulator?