Couldn't run the scheduler after handling timer 5 Interrupt

I afraid that’s not yet correct. You should e.g.
#define configLIBRARY_MAX_SYSCALL_INTERRUPT_PRIORITY 5
and use the configMAX_SYSCALL_INTERRUPT_PRIORITY macro as done in this demo example:

/* Cortex-M specific definitions. */
#ifdef __NVIC_PRIO_BITS
	/* __BVIC_PRIO_BITS will be specified when CMSIS is being used. */
	#define configPRIO_BITS       		__NVIC_PRIO_BITS
#else
	#define configPRIO_BITS       		4        /* 15 priority levels */
#endif

/* The lowest interrupt priority that can be used in a call to a "set priority"
function. */
#define configLIBRARY_LOWEST_INTERRUPT_PRIORITY			0x0f

/* The highest interrupt priority that can be used by any interrupt service
routine that makes calls to interrupt safe FreeRTOS API functions.  DO NOT CALL
INTERRUPT SAFE FREERTOS API FUNCTIONS FROM ANY INTERRUPT THAT HAS A HIGHER
PRIORITY THAN THIS! (higher priorities are lower numeric values. */
#define configLIBRARY_MAX_SYSCALL_INTERRUPT_PRIORITY	5

/* Interrupt priorities used by the kernel port layer itself.  These are generic
to all Cortex-M ports, and do not rely on any particular library functions. */
#define configKERNEL_INTERRUPT_PRIORITY 		( configLIBRARY_LOWEST_INTERRUPT_PRIORITY << (8 - configPRIO_BITS) )
/* !!!! configMAX_SYSCALL_INTERRUPT_PRIORITY must not be set to zero !!!!
See http://www.FreeRTOS.org/RTOS-Cortex-M3-M4.html. */
#define configMAX_SYSCALL_INTERRUPT_PRIORITY 	( configLIBRARY_MAX_SYSCALL_INTERRUPT_PRIORITY << (8 - configPRIO_BITS) )

And as far as I remember there is hint in the mentioned FreeRTOS docs regarding using STM32 drivers and NVIC priority grouping.

Sorry - I’m not familiar with cube. But I thought it generates all required files/configs…