> As an alternative, could x-payments upgrade be run through php script?
Actually this is what you need to do. Every owner of X-Payments 2.x downloadable license gets access to upgrade script that makes X-Payments upgrade process a lot easier. If you have X-Payments 2.x downloadable license - just check your File Area at https://secure.x-cart.com
Btw, users of hosted X-Payments accounts do not need to worry about doing upgrade themselves. They can just send us a ticket requesting to do such upgrade free of charge.