Code C1233?? Service Suspension??

You did clear it, but since it was not fixed, the fault is detected and the DTC is reset. You can find the codes here. It will obviously be a chassis code.
http://myweb.accessus.net/~090/dtcobd2.html

C1233 - Right Front Wheel Speed Circuit Open or Shorted

So what does this mean? How do I fix this?

I also found code B0429 - Temperature Control #3 Rear Circuit Range/Performance, any idea on what this entails and how I can fix it?

Thank you!!

C1233
The speed sensor is integral to the hub & bearing assembly. If it is bad, you have to change the assembly. First check that the connector is clean, tight and plugged in.

B0429
Seems to be a rather common DTC. It means that the rear air mix door is not exactly where it is commanded. In other words, it is commanded at 40 degrees open and it is reporting 42 degrees. I had the same code and the dealer tech told me that it does not take much variation to trip that code. Since I was having no problem with rear seat heat, I told them to leave it along even though it is still under warranty.

Is this something that could have been affected when I had the car alligned?

Possibly, depending on what they did, but probably not.

So what could cause this? If the assembly needs to be replaced how bad could this get?

Sometimes the sensor just fails. Not sure what you mean by "If the assembly needs to be replaced how bad could this get?"

After having to put out the money on the head gaskets I am overly sensitive to how much the repair could be. How much do you think a reasonable charge would be to replace this?

Last hub & bearing assembly I did was on my '92 Deville. Got it from Napa for $200. Took me less than an hour. I'm just guessing but I'd guess a shop would charge about $400 maybe. Dealer probably more. Check the connection first. Make sure that they didn't knock the plug loose.

edit:
Correction, last 3 I did were on a Ford Snorus. Now those took several hours.