Don't know what you mean by copying files, but it's best to tar the files with permissions from the ssh shell prompt.
tar cfvpz backupname.tar.gz *
This will create a file named backupname.tar.gz which you can download and upload to your new server. Move it to the directory, and then in ssh:
tar xfvpz backuname.tar.gz
That will unpack all the new files. If necessary, you may need to change the file ownerships. For example, if your files were domaincom.psacln before, and now they are domain2com.psacln, you'll need to change ownership with: chown -R domain2com.psacln
Then backup and restore your mysql database.
Edit your config.php
And everything should be good.
Don't do a fresh install unless your upgrading your x-cart, otherwise you'll have to reimplement all of the customizations for no reason.
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