Aside from the kernel patches, there shouldn’t be any other software changes you need to make. I shared our Linux porting guide application note in this thread if it is of benefit to you: Raspberry Pi Zero 2W WiFi HaLow Module (MM6108-MF08651-US) Integration
The pull up on SD_D2 is essential. Other pull ups on data lines are often not necessary, so long as the host is actively driving the lines (configured “push-pull”). I would recommend putting pull up resistors on these data lines during initial development, and remove them if you need to tune aggressively for power save.
The pull-up on the clock line should not be needed. However, I have seen one instance where it was. Possibly a host misbehaving - we haven’t had a chance to do a deeper analysis on the device. If you’re designing a board, I would recommend putting a footprint for a pull up on that line, but leave it unpopulated.
Please share the actual logic analyser files if you can. It allows me to more closely examine the trace.