I have been having wiring issues with my 1987 CBR600, when I got the bike it was gravity fed, I accidentally left the petcock on once and it flooded the engine and oil, I suspected stuck float in carbs so I took the float bowls off and did not find anything, so I decided to reinstall the fuel pump system and when I went to start it again with new fuel pump installed it turns out it had a bad fuel pump relay, bought a new relay and still nothing not even a click or prime, tore entire harness out and can't find the issue what could be causing this?

 

It could very well have been gravity fed for a reason, hence not working when you fitted the pump.
Have you check for the correct voltage at the relay and then the pump?
It will not prime if the float bowls are full and even then only a little until it gets going then the pump kicks in.

 

I cannot speak to your generation of bike but on the f3, the fuel pump does not begin working until the engine is running. That is by design.
again, that is the f3. Your gen may be different

 

I am unsure what the voltages are supposed to be but I think they are fine because the relay and fuel pump are brand new, i think i have narrowed the issue down the the ignition cdi because the ground wire going into it also grounds wires coming out of it including the wires going to the pulse generator which then tells the relay to kick on, i have ordered a used cdi but unsure if it will work because it is for the 1987 Honda Hurricane 1000f, i looked at both diagrams and firing orders and they seem identical.