And they said that I have wiring going from my secondary fan to my thermostat that can short circuit my radiator fan, and I have to remove it. What is the reason for the wiring like this?

If I take this wire off will it break anything in the process?
(I'm thinking of taking it out to smog it then reinstalling it)

 

Why would it break anything? And is it on the bolt that screws into your thermostat housing? If so that's just a ground. Post a picture.

 

Does it look like someone messed with the wiring at all?

 

Thats just being overly picky.
As long as the fan kicks on... heck what does the fan have to do with the smog test anyway?
they shouldnt be testing the cooling system just emissions.

 

Yeah it looks like they took 2 connectors and clamped them onto the wires leading out of the thermostat. They connect to this little black box.

And his reasoning was "if the fans fail then your emissions will rise"

 

Alright, judging by this thread: https://honda-tech.com/forums/honda-crx-ef-civic-1988-1991-3/how-can-i-hardwire-my-fan-always-run-2530498/

They were trying to hook the fan up to a switch to turn it on and off. (I always wondered what that blue switch was for) Lol

 

Of course but if it doesnt fail during the test why would he care?
Where are you being tested California?

 

Merced California. He said it was part of some regulation or some ish.

I'm just going to detach it and get it smogged.

 

Good deal... just make the man happy and get your cert.