there are minor differences between the download store and the one released to cpanel for distro. in addition some hosting companies customize the agora cpanel package. however, these differences usually do not interfere with trnasporting from one server to another.
do the web install on your new server/hosting. delete the default product images from the fresh store. delete the gateways you will not be using from the admin, library and forms folders. delete the html files you wont be using in the html folder. now upload the obvious files you'll beed to customize the store...
agora user files (store and gateways) from the admin folder, the data.file from the data_files folder, any custom files from the custom folder, storefont, options, headers and footers and ppinc, pages files, form files (gateway) and images. go to the library folder and upload any files you customized from your old store.
you can sort files by date and upload files folder by folder but, be sure the files with the most recent date are ones you customized and not ones customized by the hosting company.
don't worry about updating the pgp/gnupg files, cookies and cart files. you may want to update the sales log or at least archive the old one(s).
you can also upload the protected/misc/mgr_pass.pl file. this will set the manager user/pass to your old credentials. update any other proteced files as well.
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