The only way you could get away with it now without touching mojo code would be to implement the WebStorePayPalIPNHandler and WebStorePayPalPDTHandler in your own project with a different namespace in your own assembly/project.
The provider is loaded from config files in /Setup/ProviderConfig/paypalipnhandlers and paypalpdthandlers folders. They are loaded by name but they point to a class and assembly, if you edit those files to point to your assembly using the same provider names then it would load your version instead of the WebStore version. So you would want to copy the whole implementation from the corresponding webstore classes and then modify them in your own project to add your logic. That would be a decent temporary solution, the only thing you'd have to keep in mind is that on upgrades it would replace those provider config files so you would need to restore yours after upgrades.
Basically the way it works with PayPal is that the cart is serialized into the mp_PayPalLog table and the log id is passed to PayPal as a custom variable and is returned to us by PayPal, so we lookup the log and the log has the name of the IPNHandler and PDTHandler to load, so as long as you use the same name it will load your custom one.
As a side note part of the reason it is implemented that way with the cart being serialized into the log is so that we have a record of the cart as it was before we sent the user to PayPal. Nothing stops the user form using 2 browser tabs and adding more items to the cart after they have been redirected to PayPal, so to prevent them from getting things they did not pay for we can't just go by the cart id. ie we don't want them adding more stuff to the cart then paying for just the item that was in the cart before we sent them to paypal and getting more items for the price. So each time an item is added or removed from the cart a new record is created in mp_PayPal log with a new id, and we restore the cart to as it was before they went to PayPal when we process the notification of payment from paypal using the log id we sent with the original request.
Hope it helps,
Joe