Manual trans color
 

So I’m recently a new Honda owner. A 98 civic 5spd ex model. Love the car love the gas mileage. I started to hear a whining noise a couple days ago followed by what can only be described as a grinding noise. Okay trans is giving me problems. I’m no idiot when it comes to working on vehicles been doing it for a long time and when I went to top off the fluid in my trans which took darn near two quarts 😫 (I know that’s pretty much the entire capacity) , the fluid that came out of the fill hole was a dark red color. Please tell me that some idiot did not put atf in this and if he did what kinda damage am I looking at.

Does it still make the noise or have problems after you swapped the fluid? Old Honda trans fluid will have a dark red color to it and smell like cat piss IMO. I've been around it enough after swapping to an H22 motor and destroying axles every 6 months in my old 99 Civic to know that it smells horrendous.

What are the transmission problems? Have you checked the clutch reservoir to make sure that's at the correct level?