My son has just recovered from HF&M. For a short time he had the Dr.'s perplexed as it was not inside his mouth. His regular Pedi diagnosed it immediately.
I actually initially thought is was chicken pox as it looks very much the same. Right now where I live (I'm in Alberta) we are experiencing a great deal of HF&M, and it has "evolved" a bit. The reason they had trouble diagnosing my son initially is that classically, HF&M will show up literally only on the hands, feet and inside the mouth. My son had it around the outside of his mouth, on his hands, not as much on his feet, but also on his arms and in the diaper area which is not usual. He ran a high fever (105 at one point) off and on, had this crazy rash and was very miserable..screaming all night for 2 nights in a row. This is because it often can make their joints ache. Good news is, it is very very rarely serious and they recover fairly quickly. In my son's case, about a week.
My point in telling you all this is that HF&M has changed this year for many children, and they symptoms are not as classic as they once were necessarily. So don't dismiss HF&M if it is not exactly as described. All the best to you.
The one that comes to mind is Chicken pox and also Herpes simplex