If im understanding you right,
it sounds like your deleting files/folders that you should not have deleted.
and thats resulting in the weird errors that you would see now.
Normally you would not delete anything accept content in your public_html
folder (not the public_html folder itself)
with acceptation of the content in the tmp folder if you do a lot of deleting.
plus of course the folders/content
garrettroyce mentioned.
i beleive staff already mentioned in a previous post that deleted files would
usually purge after a certain amount of time.
as for the 403 error, i think thats caused by wrong permissions,
no .htaccess file, or you possibly deleted the domain folder related
to that website. i may be wrong on that and staff would correct me.