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.