Here is a stab in the dark.... i have experienced the same sort of performance loss (also a 3090 FE)
Has the "Activate Windows" watermark appeared in the bottom RHS of the screen since you've changed a bunch of components? Somehow that little sucker of a logo when on the screen robs 1000's of points in benchmarks and cuts game framerates (it somehow creates a phantom load on the GPU). I activated windows and all is normal. I only write this as i can see you're running out of ideas.
Nice idea as on checking in system settings my windows hadn't been activated and there was an error code. Ran the troubleshooter and it's activated. I wasn't getting any on screen warnings though before, and nothing has change re Timespy scores.