Appreciate that, we recently did a engine and transmission swap in my fiancés 2002 Accord V6, they never came in manual, and most of the people who did the manual swaps used a lot of discontinued parts or guides that are no longer available due to photobucket and such expiring their photos.
There really wasn't any how-to guides, so a lot of it we had to look thru wiring diagrams and such to figure out what to do.
We got a J32A2 from an Acura CL Type S, along with the ECU + 6 speed manual with LSD that comes with the CL-S, and then took a bunch of 4 cylinder manual accord parts and pieced everything together. Ultimately I had to repin the entire interior harness to match the ECU. Re-pinning everything wasn't a fun experience, but it works perfectly outside of reverse lockout + reverse lights. (Need to figure that one out still)