My take on this is as follows:
If you were on the EEA Family Permit since February 2007, you would have been allowed to get permanent residence via that track in February 2012. Then, had your partner not become British, you would have been able to have applied for UK citizenship a year after that.
As you know, this all became more complicated after your husband became British. I don't believe that this cancelled your EEA Family Permit as he was still Swedish. But that is a question that you might want to ask a solicitor (as Transpondia has suggested) to be sure. If it was still valid, then you would have still got permanent residence in February 2012, and then could have applied immediately for UK citizenship at that point (under current rules) because your husband was also British. That would have been the quickest way to UK citizenship for you.
Just because your husband became British, you can't just automatically switch from EU/EEA rules to UK rules without having been on the proper track in the first place. If you wanted to apply for ILR as the spouse of a British citizen after having lived in the UK for two years, you needed to have been on Limited Leave as such, by having first applied using FLR(M) two years before.
But you didn't do that. You've been on an EEA Family Permit. In that regard, your ILR application was rightfully refused. You had completed more than two years living in the UK, and yes, your husband is now a British citizen. But you were on the wrong path. You could only have applied for ILR had you been on the UK-rules path (i.e., FLR(M)) and you weren't. You were benefitting from EU/EEA provisions.
However, you were misinformed. Three times! Do you have any proof of this? Did you contact your MP and get a letter from the Home Secretary or the Minister of Immigration or the UKBA enquiry line saying that, yes, you could apply? I ask that because that will make a stronger case for an appeal. And if they do not grant your application, and they might not because it would be outside the rules, they should at least give you your money back.
I was in this situation in June 2008 when I was informed by the then-Home Secretary that I could apply for ILR. It's a long story, but I went through my MP to get that "yes-you-can-apply-now" letter, and after they refused me, I at least had the letter to say, "Hey! What gives?". I put in a complaint, and while they did maintain the refusal, they at least refunded my money. They admitted that they had made an error in saying to apply in June 2008 instead of June 2009. So the money came back, and I got ILR the following year with no problem.
One thing, though. You may now be delayed at UK passport control when you re-enter the country because of this refusal. It will pop up on your record, and for the first time at least, they will likely issue you with a IS81 while they investigate the refusal at the border. This is an annoyance, but you can complain through your MP to get that "red flag" removed from your file. Yes, this refusal is now permanently part of your immigration history, but the inconveniences associated with it (i.e., the fee and the delays at immigration) can be mitigated.
I hope that helps somewhat. I've been in a similar place as you, and it's not fun.