Ok, I figured out how to do this but you do have to rePwn it. First off, not just any .png will work. It must have a transparency layer and it will add in the black background automatically. For example, the first attached iPhoneLinux.png image will not work but the second logo.png will work and will make the same boot logo in the end. Click on the 2nd image to see what I mean about transparency as the thumbnail system on this forum also adds in a black background. Feel free to use the logo.png and recovery.png files I have attached if you wish.
What you need to do if you have already pwned is re-pwn your iPhone again. Load up QuickPwnGUI120 and do not go any further. When the program executes it will create a folder with all of the program files in C

Documents and Settings\Username\Local Settings\Temp\RarSFX1 and in that folder you should see a logo.png and recovery.png. Replace those with the proper .png files of your choosing. Then go back to QuickPwn and continue as normal, leaving the 'replace boot logos' option checked.
Hope that helps!