"I need to pull (2) 12 amp circuits and (2) 14 amp circuits through with thhn and properly box on both sides and continue with romex to isolate the circuits I need for the transfer switch."

I think you mean two 20-amp circuits (#12 wire) and two 15-amp circuits (#14) wire, so I'm operating on those assumptions.

"The NEC states with 90 Degree I should only be worried about derating if the are more than 9 current carrying devices in the pipe.

I am correct with this interpretation or do I have to derate with 70 percent for conductors of 7-9. Do the nuetrals count as a current carrying conductor?"

You are correct in concluding that derating requirements won't force you to increase conductor sizes until you exceed 9 conductors.

What sometimes leads to confusion is that when you begin derating, you start with higher potential ampacities for the wire sizes. In the case of #12 AWG copper, for example, the full ampacity is 30 amps. Although you do, in theory, derate to 70% when there are 7-9 conductors in the raceway, the ampacity allowed still doesn't drop below 20 amps (for #12) or 15 amps (for #14). Therefore, there's no practical effect of the derating when you have up to 9 wires.

Yes, with some exceptions, neutrals count as current carrying conductors. (The neutral in a multiwire branch circuit is excepted, since it only carries the imbalance of the two related hots.)

Your specs are fine and there's no need to increase wire size to #10/#12 because of derating.

Yeah. After I read it again. I realized I could have been more specific. Sort of bulleted it out without utilizing the proper terms. I appreciate your time and help. Many thanks.