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Say I want to replace the clones DC 15A with a cluster bomb gun I downloaded, how exactly would I go about doing that?

Also, after i reskin a unit where do i put the TGA file?

to learn how to do that you should read the jedicreation.doc in the modtools documentationfolder. it covers pretty much all aspects of it, including weapons.
after reskinning an unit you put the taga in the same folder as the mshfile, the mshfolder of the side your unit is in.