The best way to clean things up is to indeed copy off all of what you
want saved files, bookmarks and such. Install sbackup its a simple
backup tool that will run when ever you wish, you can include and
exclude directories. All of you email, browser other setting are
stored in hidden files in you /home/whoever directory. Under sbackup I
would backup /home/whoever to and external device (usb drive) so that
you have everything you need. Then use the livecd ubuntu and ensure
that upon installation to select USE ENTIRE DISK. This will remove the
extra partitions and install cleanly using the entire disk. Make sure
that you remove the external usb drive and select the correct drive
you wish to use.

I have used this method many times in playing and switching OS. I have
switched from Freesoire to Ubuntu on all of my machines even running
xp in vmware and virtualbox for the occasion Neanderthal regression fix.