I there, I built my F2R16-PROG, but can't find any steps documented on how to actually program my F2R16 with MiniProg. Any guidance would be much appreciated.

To flash the F2R16 with the F2R16-PROG a TL866 with the TSOP-48 adapter is required. A jumper wire should be used to connect WE#, RST# between the adapter and the F2R16. The A18 signal must also be connected when using a F2R16 with a 29F800 device.
The vendor and chip in the TL866 software should be set to the actual chip soldered on the F2R16 (most of boards from the first batch have a Fujitsu 29F400TB in TSOP 48 pacakge).