Yes, the FDTD allows to model fluorescent enhancement and numerous publications bring back this type of works. Use "fluorescence enhancement fdtd" key words in Scholar to find it.
I recommended you the book of Le Ru and Etchegoin about Raman enhancement which includes a section about fluorescence :
I have done this with MEEP. You need to find the electric field enhancement, which is relatively easy. Then you need to consider the emissions and obtain a modified quantum yield, which is normally done using a small dipole model for the flourophore molecule. I think with MEEP you can calculate the electromagnetic density of states to find the emission enhancement, but I need to do some numerical experiments and work on this to be sure. I'll try and send you some of our publications with some more detail on the calculations in the next day or so, and also a few other useful references. If we do any further work I'll let you know and maybe you can also let me know how you progress.