Can you double check those CAN pins? Because PB5 and PB13 are on almost every package on completely different sides of the chip. Now, on the CMOS side, these aren't a differential signal, but still... It seems really strange to have pairs of CAN pins all over the chip, then for the bootloader use two completely different sides of the package when at least four pairs are available on most chips. Plus, AN2606 mentions this as FDCAN1, but those pins are FDCAN2.
Also, I'm going to need you to double check the USART pins. Still doesn't look right to me. In fact, all that has changed is nothing because you only sent the TX pins, but overwrote the AN2606's RX pins.
USART2_ TX: PA3 - you
USART2_TX: PA3 - AN2606
USART2_RX: PA5 - AN2606
I'm assuming that you made a mistake and meant TX is PA2 and RX is PA3. Please confirm.
USART3_TX: PD8 - you
USART3_TX: PA4 - AN2606 (unlikely)
USART3_RX: PD9 - AN2606
I think this seems better with one issue. A few packages don't have D8/D9 pair at all. Does the bootloader on say a VQFN68 not have USART3 access?
This is not an inexpensive change if these are wrong, please confirm above! Thanks.
