Question: What I've planned to do is place an IPN script (similar to the one that comes with s2Member pro account as an extra), and set a custom payment gateway notification url to that IPN script. Now it seems the connection is happening, but there is a problem w/ post vars verification.

You can avoid this problem by passing your Proxy Key, which will automatically verify the incoming IPN; i.e., since it not actually from PayPal, s2Member needs you to pass the Proxy Key. Please see: WordPress Dashboard s2Member PayPal Options IPN Integration. There you will find a link that expands another section with additional details and an IPN URL which already contains the Proxy Key that you need.