Go to
http://europa.eu to get specific info on rights of mobility for you and your husband. Search for the pertinent ones and print them out in English and French.
Since your husband is American, go to the website of a French consulate in the US. There you will find, in English, how 3rd country nationals (Americans in this case) that are immediate relatives of EU citizens can travel to France with their EU spouse or to join their EU spouse without a visa.
You only need a visa for family reunification if you join a FRENCH national spouse (notice the difference here). 3rd country national spouses of EU citizens that do not need a visitor visa (Americans, for instance) will not need an entry visa to reunite with their EU spouse in France. Once you find this info on the French consular website, print it out.
You do not legally need to register with the préfecture as an EU citizen at this time. You can just live and work in France. You are, after all, just like any French person, an EU citizen. While your husband will need a CdS, his rights are not attached to him having or not having a CdS. It is also irrelevant how he entered France. If he has lived with you in France already, and you have exercised your treaty rights during that time, he is a legal resident of France with or without CdS.
In order for him to get a CdS now, you now have to prove that you are exercising treaty rights as an EU citizen (see the EU web-site for an explanation).
Once you have collected all the above info in print (in French and English), have collected documentation that prove your right to free circulation (work-contract, minimum of 10 hrs of work/week, or maybe you are working for yourself, going to school, are looking for work or are self sufficient), go back to the préfecture.
Now, and this is important, make sure you make them understand that you are applying for your husband under EU-treaty rights. The trouble you have may stem from the fact that the fonctionnaire, intentionally or unintentionally, does not take the difference in procedure and rights between a French national and an EU citizen into account (a huge difference, EU nationals have more rights in this respect)
This often happens, so make sure they really know. If you don't get anywhere with whomever you deal with, ask for their supervisor (and yes, they have one, and no, they did not just step out just right this moment), and try your luck with them. That will often do the trick. Be polite, but do not back down.
Again, depending on the préfecture, they just may not have many cases of EU + 3rd country national relative, and therefore be ignorant of the difference between French citizen and EU citizen famili reunification (more onerous for French citizens).
So, bonne courage, bonne chance et beaucoup des documents!