Hi, if you have been here 4 years, why are you only now apply for Residence Permit?
My wifes visa expires by the end of May
A couple of points. Firstly your wife does not have a visa, she has a permit, issued under EU regulations. Secondly, the difference is significant if only because under the terms of the EU regulations that came into force on 30.04.06, your wife has her rights irrespective of any permit issued to her. Or put it another way, any permit that is issued is merely confirmatory of the rights already possessed.
However for a non-EEA Citizen such as your wife it is actually quite useful to apply for a Residence Card, otherwise she will find it difficult for example proving that she has the right to work in the UK. But even without the Residence Card she has her EU rights and cannot be deported.
OK, what I suggest you do is that when you submit your application, which will result in a Residence Permit, you also enclose your wife's application on form EEA2. Then if the section that deals with these applications doesn't think that is the correct form, will they can say so, and the FMRS form can be submitted.