Hi,
really hard to suggest anything. You are right that on the CLK line you cannot control the slew rate in respective PCR register as it is the fast pad type, or better you can change the SRC field but it has no effect for fast pad.
You may try to decrease the QSPI speed to see if the EMC spikes moves, or disable the QSPI to know it is really the root cause. BTW 682MHz doesn't look to be a multiplied frequency of 61Mhz, maybe 62.
You can try to attenuate the high frequencies with a simple R-C low pass filter immediately after anything that drives a line. This is in part what the series resistors are doing. It forms a low pass filter with the parasitic capacitance of the line. It may be not enough. This can be fixed with some deliberate capacitance on each line. So try to put some pF as close as possible after the resistor on CLK line.
BR,
Petr