So, when I shift my manual transmission, if it isn't a super smooth shift, I get a bad rattle/popping or banging. It's coming almost directly under the clutch pedal area. I'm thinking maybe a motor mount, or suspension. I know it seems to be happening when the engine is rocking back and forth. I can't seem to duplicate it when it's parked. Any suggestions where I should start looking first. I've heard these things have suspension problems. Help!

 

The usual suspension issues are ball joints and tie-rod ends.
Your noise could be a mount or possibly the exhaust system.

 

well, I replaced the sway bar bushings. wasn't those. Gonna slowly replace all the suspension parts as I have extra cash. Next will be sway bar end links, then control arms.

 

Take it in for an alignment. They will tell you if you have any bad components.