I'm not completely sure what aspect of the GPU upgrade would be related to the issues you are having. This might just be a more general High Sierra problem.
I have always used APFS with 10.13.6 on my SSD. I haven't noticed any issues with this configuration. If you really wanted, you could try to wipe the High Sierra installation again, and format the SSD with APFS, to begin with. This may fix things. You'd just need to use the disk utility program on the installer USB to erase the drive and reformat it as APFS. My understanding is that APFS is more appropriate than HFS+ for SSD drives anyway, hence why the computer automatically upgraded to it.
Perhaps before trying this, the customary zapping of PRAM and the SMC would be in order first? You could also try making a fresh Catalina Loader on another USB (so as to preserve your mostly functional USB), and check if that helps at all.
As it sounds like your computer was working quite well for a while, as long as the hardware has remained the same, I think it is more than likely that you can make the software functional again (it might take quite a bit of experimenting, though).