Clunking/Knocking noise

Ok, first of all, this is not coming from the engine bay at all.

It seems to be right underneath me and the passanger. Its just a knocking kind of noise, like someone is underneath my car hitting it when a wrench or something. I was thinking it was my exhaust at first, but when I was at jiffy lube getting an oil change I was down in the fit fucking with stuff (my buddy works at the lube so i get free oil changes and do whatever i want to my car) I was shaking around my exhaust and it seems to be hung just fine. So then I went to look at the suspention, I started wiggling stuff around and still couldn't find anything moving around. Then when I was kinda stumped I just looked up and looked at my shift linkage, on closer inspection, I noticed that my bushings are past shot and the linkage has a good amount of room to shake around because of it. This noise is really getting on my nerves and I'd like to get it fixed. Is it possible that it could be my linkage? It mainly happens when Im cruising at speed and going over some bumps. And its like a fast knock, like maybe 2-3 knocks per second. Any help would be awesome.

Thanks guys.

If the shifter bushings are worn, that would be a good place to start. www.summitsportcompact.com has Energy Suspension poly bushings for $10.00. For suspension inspections, the best way is to raise the front of vehicle so no weight is on the tires. Then grab the tires trying to shake in all direction - that method usually shows bad ball joints, tie rods, or bushings which all could cause a similar noise as described above.