I have not read over this entire thread, but here is what I think.

1.) Linux should have an anti-virus to keep from passing viruses to
other (non Linux/ Ubuntu users.)

2.) Put Ubuntu on the machine with the default setup and run updates
and the machine should stay secure. Don't
install any software not from Ubuntu servers. (More secure packages.)

3.) Change all your email addresses, logins, password, and change your
Internet Service Provider.
They can't hack your stuff if you disappear. Start a new web persona.