Here is something to consider.. It's a hand made guitar, and the pickguard appears to have been manually cut from a sheet of material. It looks like the hole for the neck pickup needs to be rounded out a tiny bit. When the builder installed the pickup, he left the lower pickup screw a little bit high, because the lower end of the pickup is getting jammed up on the plastic when you try to lower the pickup height. It was probably satisfactory before he tightened the screw. The OP started cranking the screw down which caused the bottom corner of the pickup to get bound up against the plastic pickguard. You can see how it's tilted because of the pressure it is causing up against the pickguard. As he strums hard on the strings, or rattle the switches and knobs around trying to isolate the noise, the pickguard is flexing slightly causing a creaking sound. That can sound horrendous through a pickup and amplified.