I have a 87 Toyota 4x4 with a 22r and IFS. The problem that I am having is a clicking noise in gears from 1-3 in 4th it goes away. It also goes away when I push in the clutch, so I really don't know what it could be or where to start. I have checked the u joints brakes and things like that but really don't know what to check next. Any help would be great.

 

check your fluid in the tranny. check plug will be on the side.

 

You stated the noise goes away when you push in the clutch.. could be your t/o bearing causing the tick. Try to isolate the noise under varying conditions..loading the trans uphill/downhill/rolling in neutral etc.

 

4th gear is straight through, so if it is quiet in 4th or with the clutch in, but happens in every other gear including neutral, then it is probably something in the countershaft of your transmission. I had a Tacoma that whined in every gear except 4th, and I suspected the countershaft, then a Toyota tech listened to it and agreed. You can try putting the transfer case in neutral and run it through the gears to help isolate it. That would rule out U joints and the differential if it still makes the noise. With the transfer case in neutral, if it still makes the noise, chock the wheels good and crawl under the truck with a mechanic's stethescope or screwdriver against your ear and see if you can isolate where the noise is coming from.

I also agree to check your fluids.