Ok, I am not familiar with that particular hardware configuration. Perhaps someone else here will know more.
From what little I know about it: First of all, it is unusual for scope data to be sent via an RS-232 port -- there is a lot of data there and not much bandwidth. But perhaps the RS232 port is used to merely let the PanAdapter know where center freq is, and it may get the RF sample elsewhere. If that is the case, a simple Y cable may work.
http://hosenose.com/stor...mp;PrimaryCatID=46&
I would pick up the phone and call (or email) the makers of the Panadapter and say "Hey, I have an FT-5000. I am using the CAT feature to talk to my logging program. How do I set up the Panadapter?"
Let us know.
Tnx & 73,
DH