SP-404MK2: Can I sample only the external input audio while a pattern plays back?

Yes. On the SP-404MK2, set "ROUTING" to "ExtIn" to sample only the external input while a pattern plays back in the background.

Follow the steps in "Sampling a pattern (RESAMPLE)" in the SP-404MKII Reference Manual. In step 4, set "ROUTING" to "ExtIn" instead of "Mix".