I think you can not remove “custom” attribute, and it must contain at least the domain of your site, to be possible s2M to recognize the Paypal notification. Thus I suggest to re-build the s2M payment shortcodes after the problem with URLs are set, so it will put the right info in “custom” attribute.
Mark, the records you mentioned are DNS related. You (maybe) need settings of your WEB server software, thus I suggest you to call hosting admins. You (usually, as hosting customer) have no access to this area. Except you are on a dedicated server, but still it’s better to ask admins to help you.
Well, I am curious to know how exactly you fix the problem, so please post the solution later.