USB resistor locations
I haven't fully found the solution to my problem, but I have been looking at the example schematic for the particular chip I'm designing around. They have the ordering that it goes from chip to termination resistors to the speed select pull up resistor and then to the USB port. So it doesn't fully answer the question of whether ordering is important, but for the time being it at least confirms a correct implementation.

P.S. the funky transistor setup if anyone's interested is for a software reset on the USB device. R12 and R10 are biasing resistors and it's natively on, then turns off when a bit is written to the USB_RENUMn register. So you can soft reset the device without unplugging the cable.