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Check your heat shields?
Manifold might be cracked

 
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I can't hear squat in the video, maybe it's just this laptop.
Based on written description alone I'd expect exhaust leaks in the area of the manifold. More investigation needed?

 
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Did you figure this out yet? Start with simple things first, like heat shields. My D17A2 started to do the same thing for no reason a few years ago. It ticked like yours when revving it up, but not at idle or while cruising at a low RPM. I narrowed it down to cylinder number 2 by unplugging the coils while the motor was running. When I shut off cylinder 2, the noise stopped. I'm not sure what exactly was making that noise, I think it was a piston or wrist pin. But I do know that a few months later, the motor started making horrible noises going down the highway, and a few minutes later, it blew up. When I tore the engine down, I found that the number 2 piston fell apart while I was driving, and the rod put a hole in the block. Hopefully yours is something simple though.

 
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Ok, let me know if you need any help. I'm always willing to help.

 
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Well you might have helped me. Have had the car for two years now, long story short it was almost impossible to hear anything with input shaft bearing bad. After I rebuilt the transmission this summer. I have noticed a weird tick in the motor so I'll have to test it. Thank you

 
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It probably needs a valve adjustment. Honda engines need a valve adjustment from time to time since they have a solid valvetrain. The spec is 9 thousandths of an inch for the intake, and 11 thousandths for the exhaust. The valve adjustment may not be it, but it's a good place to start since it's free, easy, and relatively quick.