Perhaps someone else sent them correspondence.

Perhaps. The proper procedure is to get an I-551 stamp in your passport before you go.

If you are a US citizen, she does not need to be in legal status to qualify for adjustment of status.

They could try to do that, but most likely they will not do anything.

You should discuss it with your DSO. The DSO has all of your required information to advise you what you are allowed to do.

You should put your current annual income as of the date you sign the form. Calculate the income you expect to receive from all of your jobs.

You can file five years after you got the green card. If you were married for two years when you got the green card, there was no mistake.

If your request for change of status to H1b was approved, you are in status and you do not need any new I-94.

If you filed an I-140, it could very well be a problem for your wife to get an F2.

If you have advance parole, generally you are allowed to travel outside the US and return. But not always. For example if you have a removal...