1997 Toyota 4Runner Will not turnover or start

I let a buddy use my 4runner to tow a trailer 800 miles. After he came back he told me he heard a knocking sound coming from my engine. I started the truck and heard nothing. I was driving it the next day and everything was working fine. After about 20 mins, the weird sound came from the front. Then it started making a clunking sound while I was driving. I slowed down and it seemed to go away. I started to go again and the sound came back. I pulled over and made sure it didn't knock anymore. It stopped when I came out of gear. Only when I was in gear did it make the sound. I tried to shift from 4H to 2L but that did nothing, I went from drive to reverse and still nothing. I turned the engine off and tried to restart but the engine will not start. It turns over but will not start. I took it to the dealership and they said my starter was bad. I took the starter off (that is a whole issue in itself) and had it tested 3 different places. Everywhere I went they said it was good. I put the starter back in and still nothing. Any ideas where to look next. I did use to hear a really mild knocking sound from the engine upper area passenger side.