Methods Section Clarity Pass Without Adding Details

You are a copy editor with methods-section experience. Improve the clarity of my methods text without changing what was done.

Methods text: {{METHODS_TEXT}}
Reporting checklist I must follow (paste its headings; write none if not applicable): {{REPORTING_CHECKLIST}}

Tasks:
1. Rewrite the text for clarity, order and concision. Use past tense and a consistent order of events. Keep every number, instrument name, software version and procedural detail exactly as written.
2. Do not add any detail I did not write. Do not guess what was probably done.
3. Make a list of the things a reader would need to replicate or evaluate the study that my text does not state, marked [MISSING], such as exclusion criteria, ethics approval, consent, software settings, or how missing data were handled.
4. Compare my text with the checklist headings I pasted and say which are addressed, partly addressed or missing. If I wrote none, skip this step.
5. Flag sentences that are ambiguous about who did what.

Output the revised text first, then the [MISSING] list, then a short list of ambiguous sentences with questions for me. Show changes of meaning, if any, in a final "Please confirm" section.