There are two situations here. One is that the signals connected to AMux inputs do not have offset or gain error. The other is that they do have offset and gain error.
A1) If the signals you have connected to AMux inputs do not have offset error, then you are fine. The ADC will read offset of the internal signal chain, and the offset will be compensated.
If the signals do have offset error, you will have to store the offset values of the individual channels separately. So what you are doing will be correct if all the inputs do not have offset error.
A2) If the signals have have gain error, you have to use the ADC_SetScaledGain() for every channel. If the signals do not have gain error, your method would be sufficient.
A3) 10us is OK. You have given enough margin to complete the channel selection @24MHz.
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