7th gen civics have the D 17 engine, and the few that have had engine swaps have had the K20 engine put in. if you do that, seeing as you want a stick, just get the whole swap (engine and tranny). otherwise your gonna be messing with a gearbox to get it to get 6 gears out of 5.
heres a link to site that did the k20 swap into a 7th gen its the 7th gen SI but it shouldnt be too different
http://tech.hybridgarage.com/tech/7gtech/7g-swap.htm