One thing you could test that might improve the SA-1 detection is to slow the Master Clock:
void setup() {
...
// Set Clock Generator CLK0 to 21.477272MHz
//TESTING 10.738636MHz for SA-1 Carts (21.47727MHz/2)
clockgen.set_freq(1073863600ULL, SI5351_PLL_FIXED, SI5351_CLK0);
// clockgen.set_freq(2147727200ULL, SI5351_PLL_FIXED, SI5351_CLK0);
...
}
The slower Master Clock appears to work with all of the carts that I have on hand including the SPC7110 carts. I've also written code to set the clock correction without an external frequency counter but it needs more testing.
Make sure you have a solid, stable power supply to the reader. The SA-1 cart is one of the enhanced carts that won't work off a flaky power supply.
Good Luck!