After having enough of Windows' instability, I have decided to migrate to Ubuntu permanently. I have Ubuntu installed through Wubi and I am wondering if there is a painless way to delete windows files. Thank you.
I typically have folks run a Wubi install for a week or so before migrating to be sure. From where you are I would suggest the following route to a dual boot system.
Remove the Wubi install using normal Windows remove software procedures.
Remove large un needed files from your windows system.
Use a good defragger to consolidate the files on the windows install.
Use a live boot Ubuntu USB and GParted to shrink the windows install partition to a reasonable minimum, I say this because it is already installed and you never know when having a windows system available to test something or whatever will come in handy.
Install Ubuntu in the un-used physical disk space. Ubuntu will become the default boot and will be the fully functioning primary system with no restrictions. You may be like me and never boot Windows again, or you might find a reason to use it for something on rare occasions, whatever the reason, it only costs a few Gb.
With regard to the boot loader question. If you install Windows first and then let Ubuntu take care of the dual boot afterward during it's own install, or if you just completely delete windows by way of the Ubuntu installer (It will give you the "use entire disk" option), Ubuntu will install it's own boot loader and if it is a dual boot system manage handing a Windows boot over when it starts up.