With all the information out there on modding the Switch, and the fact that the SXOS site seriously tells you how to do it step by step and provides you with all the files(my 9 year old nephew did it all on his own), I don't think you should be modding any systems.
I think deleting WIFI settings is just an extra measure in case the system is taken out of airplane mode. My nephew took my PS Vita off wifi mode and updated the firmware. If I didn't have the wifi settings saved it would have never happened and I wouldn't have had to swap out the mainboard for...
I don't know if this is true, I run a 2tb hard drive direct to the Switch without having the charger hooked up to it. It works fine this way. I also tried it with a powered USB hub and there was no difference as far as hard drive reading times.
Are your games in XCI or NSP format? XCI goes in the root of the folder, NSP go either in the SXOS or SWITCH folder, I am sorry I don't have my system here to double check which one.
If you are capable, just open the drive up and clean out all the dust inside. It's just a dirty drive no big modifications needed. There are tons of videos online and it's pretty easy to do.
Something could have transfered over bad during install. If I do a USB install I luckily never have problems. Transfering over wifi is hit or miss. Maybe reinstall and try again.