Qsys / Platform Designer - Using IP (i.e. FIFO) in Custom Component

I'm not sure what you're trying to accomplish here. Can't you create the custom component without the FIFO and then just connect to it in Platform Designer? You could create a small system of just your custom component and the FIFO and then add that system's .qsys file to any other design (it will appear in the IP Catalog for another Platform Designer project if PD can see the .qsys file). Remember you can create systems of systems with Platform Designer.