So I have a 93 honda civic vx I recently bought. It's a manual and the other day i had my foot on the clutch cruising down a hill and the car made a grinding noise, and this happened a couple times. Then the car started having problems going into reverse or 5th and a weird noise while in gear almost like a faint tin whining noise. The noise isn't coming from the clutch it's came from the shifter which I haven't heard of before. Any ideas ?

 

Clutch in and in what gear going how fast?

Also don't cluch in to coast. Leave it in gear and take advantage of fuel cut decel. The VX with the tall gearing is great for this.

Probably input shaft bearings, all D series need them.

 

Agree about it likely being the ISB. My VX did the same thing about 20 years ago. The tinny whine you are hearing is likely metal-on-metal contact within the transmission. The reason you can't go into 5th and reverse is likely the broke parts piling up under the change holder inside the transmission. When my ISB exploded, it took out the input shaft seal too, and I was getting transmission oil leaking out from between the bellhousing and the engine block.

Depending on your level of comfort working on things, it's time to either take it to a shop or pull the transmission and open it up and see what you've got.