The notes for vaxherd's any% route simply state what to do if starting from empty save RAM, but don't say anything about how to do this. I tried starting a run by deleting all files and creating the starting files required but this yielded incorrect stats for my new characters. I am assuming the discard counter is what needs to be reset, I tried setting the discard counter used in the glitchless category and indeed got different character stats, but still not the right ones.

Could someone please state in explicit detail what is required to set up an NES cartridge from any state to execute this run? I imagine it will be useful for new runners to be able to find this information here as well. Many thanks in advance.

You cannot achieve an empty RAM state with a cartridge that's been powered on and has a working battery. However an empty RAM state isn't necessary, your assumption was correct in you only need the correct discard counter. Here is a quick and dirty way to set your cartridge up for true any% runs:

1. delete all saves and reset
2. create log 1 name: A sex: male MS: 8
3. Buy 2 wings
4. save at luisa
5. reset
6. create log 2 name: E? sex: female MS: 5
7. reset
8. Change message speed to 5 on log2 (should already be on 5)
9. continue log 1 (seed lock is loaded)
10. walk to reeve (no encounters)
11. wing to aliahan and save with Luisa
12. reset
13. Change message speed to 5 on log2 (same as above)
14. continue log 1
15. Immediately wing to reeve and walk DOWN
16. walk til you get a battle (black raven x1 and slime x1), attack and reset
17. repeat 13-16 one more time for 2 total.
18. change log 2 message speed to 3 and load log 1.
19. wing to reeve,walk south til encounter (slime x1 and black raven x4), attack and reset
20. delete all log files
21. reset

Step 1-15 are lax while steps 15, 16, 17, 19 are precise and any misstep or menu mistake requires a reset and try again

Trimmed the fat a little bit.

1. delete log 1
2. create log 1 name: A sex: male MS: 8
3. Buy 2 wings
4. save at luisa and reset
5. Change message speed to 5 on log2 (should already be on 5)
6. continue log 1 (seed lock is loaded)
7. walk to reeve (no encounters)
8. wing to aliahan and save with Luisa
9. reset
10. Change message speed to 5 on log2, continue log 1
11. Immediately wing to reeve and walk DOWN
12. walk til you get a battle (black raven x1 and slime x1), attack and reset
13. repeat 10-12 one more time for 2 total.
14. change log 2 message speed to 3 and load log 1.
15. wing to reeve, walk south til encounter (slime x1 and black raven x4), attack and reset
16. delete log 1
17. reset setup is complete, continue using "IF STARTING FROM A PREVIOUS RUN" section of the notes

This setup assumes you already have log files from previous runs, if you do not, use the previous post's setup.