My question has to do with the LSB transmitted first part. Is this standard in a typical Serial.print command or would I have to format the serial data differently before sending out the serial lines? and the corresponding receive?
If that question means: Is the ATmega328's USART sending a bit LSB first? That answer is: yes.
If your hardware is doing the inversion (in SDI-12 1 means 0V and 0 means 5V, page 3 of http://www.aquatrak.com/Downloads/SDI-12_version1_3.pdf
) you should be fine.