Debugging tool for the FTDI FT2232H in Sync FIFO mode
I've got a test utility that I made for an application that uses a 245 FIFO. You can download the source code for my test program here. It's written in Visual C# Express 2010, which you can download quickly and free to make whatever modifications you want. 

As you can see in the picture below, the test utility is extremely specific to my application, so it won't be very useful to you without some minor mods, but my guess is that you could adapt it to do what you want in an hour or two. You can look at the ReadRegister and WriteRegister functions to see how to read/write from the device.

HOWEVER
I use the D2XX drivers and I'm pretty sure that I can still access the virtual comm port through a terminal program. So I'm not sure that you really need a D2XX based tool. 

Let me know if you need any guidance.