Best not to really start/try to start your PC without cooling on the CPU. Doesn't matter which sys_fan header the case fans are connected too.
When you say 'now it works' I'm assuming you mean the case fan and not the entire PC yet?
Yeah I only swapped over the fans for like 10 second to see what would happen then put them back. The pc is still not working.
Currently looking at new motherboards as I think that's where the issue may be.