How can a custom MCU board be brought up without changing several unknowns at once?

Start with inspection and the documented power and reset requirements for the exact MCU. Measure rails and reset behavior before relying on firmware output. Confirm assembly orientation, required passive components and the intended boot configuration against the schematic.

Establish a debug or documented programming connection and run the smallest suitable test from the intended memory. Use a known pin or debugger observation before adding serial output, because a missing UART message can be caused by its own pin mux, clock or connector problem.

Add one peripheral at a time and keep a log of board revision, firmware and measurements. For an RTOS-based design, distinguish the SoC support from board-specific devicetree and configuration. A reproducible minimal failure is much easier to diagnose than an untested full application.