Hate to spread doom and gloom but i had this issue. No one, i mean no one ever had any idea on what happened or how to fix it. I hand inspected every inch of the wiring harness under hood with the Engine removed, i replaced the entire fuse box twice and took the entire ignition system to OEM including an OEM honda distributor. never got it fixed.

For me it happened when i installed MSD everything. 6AL box, Coil and cap and pretty much immediately had the issue. I called MSD and double checked the install and had 2 other ASE cert'd tech's look over it as well and it was fairly straight forward and text book. My effects were minimal at first with just what i called the Disco show. My lights would pulse and you could sorta hear the engine vary a little with the pulse. This was only for the first few minutes or so of driving the car. When the car was first started it would run nice and lean like it was supposed to, however the warmer it got and longer you drove it it would richen up. To the point where when the lights would pulse bright and stay that way you could smell the gas in teh exhaust fumes. After that the lights would go bright and stay that way and the car would drive ok but just fall on its face under 3500, if you didn't wait till the lights stopped pulsing however it apparently wouldn't be charging the battery and the car would eventually drain the battery. BTW, i had my battery and Alt checked as well and even replaced the Alt for grins and giggles.

Eventually it got worse and worse to the point where the SPedo stopped working most of the time and even with a Chipped ECU with a basemap and another chip with the same tune just with the ELD disabled in Chrome i still had the issue. that made me not want to turbo it as i couldn't keep the Fuel solid. I eventually sold the car, it was a combo of getting tired of dealing with it and just wanting something else since i wasn't going to turbo it.

TL;DR ~ Your Car has AIDS. Happened to me and it Sucked hard. I pee'd on the car and sold it after much headache and got my moneys worth out of the failbox.