So i had my car in the air on jackstands for a month doing minor exhaust repairs. I decided while its down to change the manual transmission fluid, i put 2.1 quarts of GM Sycromesh in. I start my car afterwards and go to drive it and it makes this horrible clunking noise when i put it into 2nd gear, every other gear works fine. At idle it makes the cliking sound, but very lightly. Has anyone ever had this happen before, the tanny worked fine before i parked it for a month.

you said it makes a clicking sound at idle. Maybe your exhaust hangers could be loose and tapping something check that out.

why would it do it in 2nd gear and not any other gear? Im absolutly sure its comming from inside the tranny.