thanks. this information helps me a lot.. i went to a junk yard today. and they had a 96 hatch back civic all manual with d series engine and trany. they told me exactly the parts that you listed. and they gave me a deal. 550$ for everything the trany with the shift linkage and the manual ECU, trany mounts, pedals and axles. they also told me that they will give me a 30 day warranty on the parts which is awesome cause that way i can really test the trany.
im getting my money straight this friday to get all the parts to start this project.
thank you guys a lot.
oh! and do you know a link or some where that i can get a workshop manual for 96-00 civic. i work very well with picture diagrams.