The threads on vB.com contain the information about what has changed between versions. Literally start with the 3.0.8 release announcement and carry out the changing listed in there, and continue through all the 3.0 release threads then the 3.5.0 beta (I think it started with beta 3) then 3.5.0 RC's then continue to 3.5.4
It will take a good while, so make sure that you have plenty of time, and don't miss any step otherwise something will still be broken.
If something still doesn't work after all the edits via the announcment threads, then you will need to contact whoever made your skin to see if they have a 3.5.x version.
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