How would one write a proficiency and conduct rebuttal?

First and foremost, be able to articulate why you disagree with a specific point, and with the score in general. Things like PFT (1st class or 285+), Rifle Qual (Expert) all work in your favor on Pro.

Be able to cite examples of why it is incorrect using logic and reason, and avoid emotion where possible.

Remember that Proficiency & Conduct are Subjective to a degree, and without formal documentation, the range is significantly more narrow (4.0-5.0)

Use previous marks to establish a window. If you were at 4.5/4.5 previously, and the marks are being lowered to 4.0/4.0, request documentation to show when, where, and why the opinion has changed so drastically.

Remember, this is also your counselling session, and feedback is INVITED, and it is not necessarily a firm number until after the session. You may be able to present information that had been forgotten or poorly documented to raise the scores, like LoA, CerComs, etc.

Stick to the facts... Leave your feelings out of it, and take responsibility for what was your/their fault. Lastly don't blame other people.

The pro/con system in the Marine corps is flawed, I ha earn where a NCO or SNCO like a marine and give them inflated markings. So I would say stick to the facts, the corps has standards as long as that marine makes the standards then he is an average Marine.