What is the best way to go about installing the stand alone version of coppermine with being able to keep my album structure pictures and comments?
I have no idea, since I don't know the nuke version. There's no converter available afaik. I suggest you do a standalone install as suggested in the docs and then take a look at the table structures. It might be possible to export the nuke tables and import them into the standalone, but like I said: I have no idea of the nuke port, you will have to find out for yourself.
Joachim