Hey Dave I'm glad you enjoyed the using the program on your 396. The 245 uses a really different programming language then the other uniden scanners and being that I don't have on here to play its not really possible for me to figure out how to program for it "blindly". But if you go to the radio ref wiki page at
http://wiki.radioreference.com/index.php/BC245XLT there has already been quite a bit of software created, if you havent seen that already.
As for the COM ports, yes you can usually re assign them. I am assuming you mean you have a usb adaptor that changes COM port depending on what usb port its in, since its pretty unusual to see 3 com ports on the front of a PC. In that case what you need to do is after you plug it in, goto device manager, select the COM port and then settings and dig in and somewhere there it should let you pick out which COM port you want to assign it to. I hope that helps.