On a strictly technical level there is nothing in ZC that Would cause those changes on pay pal's side to hurt the Zen Cart software.
If the problem is really and truly a direct result of PayPals change, then you can't fix your Problems by doing anything in ZC unless you've altered the core code to create specific direct dependencies.
So, the symptoms you describe must be caused by something else. Either a hosting/firewall problem (which is what PayPal's article is written towards) or a completely different thing.
Notwithstanding v139 has been out for a very long time. If you keep putting off the upgrade you're just setting yourself up to be hacked.
And, indeed, as has been pointed out already, your current problems might actually be a direct result of using old software and getting hacked. Have you even checked?



