THe only way you can keep a manual would be to use an Acura 6 speed tranny.
If you have all the stuff from your friends car you will still need alot of work. You may need to even switch out axles and such. In this particlar situation. Unless you are very mechanically knowledgable about the Accords mechanical, which this quesiton would lead me to doubt, this would be a pointless swap. You would also need the v6 HVAC controls. In 'this case' just get a V6 and move on. These parts are more useful to someone with a v6 car then a 4cyl.
Besides a Manual 4-cylinder is not that much slower then an auto V6 in the gen 6 cars. As a corner carver would go the 4cyl may even be better because you aren't pulling all that bulky V6 weight. I'd stick with your 4-cylinder setup and help your bud part out his car.