Hi,
the best way is to jump to the application right after reset. The startup code should only check a condition if bootloader or application should be started and then jump there without further initialization.
If you jump to the application later in the code, it is a must to disable interrupts on all levels (MSR[EE], priorities, local enable bits in peripherals) and it's also highly recommended to put all used resources back to default reset state.
There's no PSP/MSP on the PowerPC. R1 register is used as a stack and it is supposed to be initialized by startup code. So, you do not need to care about the stack.
Regards,
Lukas