Hi, it would seem the next step would be to turn on debugging in the PayPal module. From the perldoc:

DEBUGGING

You can see the raw SOAP XML sent and received by Business::PayPal::AP
+I by setting its $Debug variable:

$Business::PayPal::API::Debug = 1;
$pp->SetExpressCheckout( %args );

this will print the XML being sent, and dump a Perl data structure of 
+the SOM received on STDERR (so check your error_log if running inside
+ a web server).

If anyone knows how to turn a SOAP::SOM object into XML without settin
+g outputxml(), let me know.
[download]

There is also a section in the perldoc on Error Handling. You might want to setup more error checking in your code to find the cause of the timeout.