Hello, my name is Ali

I've got a 1998 Honda Civic EJ9 4-door sedan with a diabolical parasitic draw.
When I measure the draw at full battery charge it says 70mA initially but then jumps up to 3.5A, it sometimes goes down to 70mA again but then goes back up. When the battery discharged down to something like 9V the 3.5A draw also falls down to about 2.5V. (The discharged takes 2-3 hours)

So far I have check every single fuse 2 times, once by pulling each one and checking if the drain disappears and once by checking the mV across every fuse. None of them was the cause. I also check the trunk and glove department lights, but there were none. Finally I tried removing the alternator wire connected to the positive terminal of the battery, but the drain didn't change.

I have noticed that every time I connect the multimeter probes between the GND cable and the negative battery terminal (To check the drain/draw) a sound appears from the right side of the engine bay. It sounds like a small hollow wooden piece hitting something, something like a brighter and lighter version of the first sound in this video:

I'm very new to cars and I don't know all the cool terms yet (But I do know some electronics), so please explain in as much detail as you have patience for.
Any help is appreciated.

 

I had a similar parasitic drain on my Miata. Turned out to be the alternator. Have you tried unplugging that while conducting your tests?