Nothing really. Nothing of that sort is absolutely necessary for a manual swap. All that is necessary is to get rid of the trans stuff so you don't have a constant 6+ error codes and MIL light. Even that isn't really necessary as you can drive fine with no tune changes as long as the PCM is wired to think it's in D at all times. I'm going to leave fueling and timing up to a ZZP remote tune once I switch over to E85, no sense in messing with it now.
Other than that, I think the F23 speed sensor is slightly off from the 4T65E as it would read 70 when I was going 73-74, so I adjusted that to match GPS speed.
On a side note, I have been looking into extending the clutch master cylinder rod about 1" behind the clutch pedal as the pedal hits the firewall before it's fully pressed, so it might only be 90% released each time which I hope isn't causing extra wear.