You might check to see if you have an exhaust leak. I've seen leaks between the manifold and head that remarkably sound metallic. Some friends and I were positive we had a stuck lifter on a Pathfinder only to discover one of the exhaust studs had broken and the noise was coming from it huffing exhaust gasses.
I would be surprised if it is anything to do with the A/C. The compressor is on the right hand side, at the lower front of the engine.
I am wondering if it might just be that the lifters need to be readjusted. When they are loose, they tend to make a sort of clatter sound. They also could become a little quieter as they warm up, because of the metals warming up. I'd check that out.
I want to take it to a Honda garage and see what they have to say about it. Even if it's something kind of expensive the car is still worth it to me. Hopefully it is something that I can attempt myself over the coming winter months.
I plan to be taking the A/C system out when I have the chance.
Why not just leave the A/C system in? Unless you turn it on to run it, it just sits there and acts as an idler pully for the belt for the A/C. It basically doesn't cost you anything to speak of, unless you use it.
I don't have anything against you taking it out. I have one that I'd like to put into mine, because it can be a lot more comfortable to drive when it gets really hot.