Connecting separately powered devices via serial
I think I can answer this one myself. My main issue was knowing whether or not 500uA flowing into the FTDI chip will damage it but I think the best idea is to avoid having to ask that question.

If I use a voltage divider from the main USB line to an analog comparator or a2d or even a high value pullup to a logic input on the PIC micro, then I can detect if USB power is present or not. If not I can tristate the serial port.

Other than that, googling reveals that using the diode and pull up to RX works just fine to prevent current flowing the wrong way...