One thing with the stem, remove stem and check there aren’t any black marks on the steerer from the headset compression washer. I had a road bike that did this – the micro movements between the compression washer and the stam would ‘mark’ the steerer with aluminium deposits that were black. Wire wool on both parts and a clean up, re-grease, and it would be OK for 12 months, then start again – this was a daily use bike)
Same happens with plastic road cleats, you get aluminium marks on the plastic, and after time, this causes the pedals/cleat to creak.
Rear pivot bearings are prone to creak too due to lack of movement.