Is it possible for me to install to the Hard Drive from the persistence partition ? I've made a lot of progress in the configuration, but don't think I need to use the USB anymore (slow). I don't want to overwrite the windows install, either (I want to dual boot).
Thinking out of the box, I would install Elive plain beside windows an copy in a third live mode die /home to the fresh install.
Regarding of your changes at the system, the following will be more or less complex.
It may be tricky to copy /etc because of some differences. But you should take a look at the diff of /etc/groups and /etc/shadow, to avoid user-missmatches. The filesystem is only knowing UID and GID, not the names. so a UID 1000 can be a different user on different systems. On debian-based systems the user should be 1000 counting up, but also the system users shouldn't be mixed up.
I do like the old 'mint' way of upgrade:
- save list of installed packages
- backup /home
- reinstall new version of mint
- restore list of installed packages
- restore /home
See: How to backup settings and list of installed packages - Ask Ubuntu
So my wife got an extra external harddrive for this process. And because she isn't much interested in backup her data, at least I have a yearly snapshot of her system, pre-upgrade 
It can be done, albeit that I don't see any benefits there. 
"Just" a matter of copying the USB to disk and fooling the chainloader that it has to be booted as a flashdrive.
Slax used to enable that.
There's more sense in running the USB from virtualbox fullscreen mode ..... and the most sense is still to reserve some space next to windows and do dual-boot.
Edit.
I did think of a single benefit:
On a machine with sufficient RAM you could run Elive solely in RAM and on "shutdown, save to persistence.....you could do that from USB on the same machine too though. 
