It seems I'm missing these PPL3 defines (lifted from NUCLEO_H743ZI/mpconfigboard.h)
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// The USB clock is set using PLL3
#define MICROPY_HW_CLK_PLL3M (4)
#define MICROPY_HW_CLK_PLL3N (120)
#define MICROPY_HW_CLK_PLL3P (2)
#define MICROPY_HW_CLK_PLL3Q (5)
#define MICROPY_HW_CLK_PLL3R (2)
I did find this is one of the C examples that shipped with the board.
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Stm32_Clock_Init(160,5,2,4) // 400MHz
Stm32_Clock_Init(u32 plln, u32 pllm, u32 pllp, u32 pllq)
I need to get my hands on that graphical clock calculator tool you mentioned @jimmo