okay lots of information for me (given I am not very familiar with the JROX Jam affiliate program 
I will try to answer as best as I can.
1) You can use the “custom” variable of PayPal to pass the cookie variable. custom variable is a pass thru variable.
2) Yes you can have more than one script using the IPN but not at the same time. What is means is that PayPal won’t send the IPN to two scripts after the payment for a particular payment. You can specify the IPN URL in your profile but as soon as you use the “notify_url” variable specifying the IPN URL for a button it will get overriden (eStore does this).
3) The simple shopping cart doesn’t use the IPN feature as it doesn’t do any post payment processing work. You can turn of the IPN in eStore so it acts like the simple shopping cart but you won’t get all the features of eStore (eg. automatic delivery of digital products via email).
I think one of these two methods might be a feasible integration option:
a) System Integration using a PHP script.
b) Forward the IPN received by eStore to the JROX system. (http://jam.jrox.com/docs/index.php?article=114)
step (a) sounds easier. Here are the name of the variables that you will need.
total amount = mc_gross
transaction ID = txn_id
The “mc_gross” field will have the total amount and the “txn_id” field will have the transaction id.
Is there example code available for this integration option from the JROX Jam affiliate program?