Email is a great way of communicating for business.
However, it has its drawbacks. Most of these stem from a lack of clear communication.
Get to the point. If you need to introduce yourself and your reason for emailing, do so in the first paragraph. Keep it simple. Your reader doesn't need to know your whole life story, just your reasons for emailing.
Lay out your topics/questions in an orderly fashion - not just stream of conciousness. If you need to get all your ideas down quickly, do so, but then edit what you have written to make logical sense.
Use paragraphs to define separate topics, issues, etc. It is very hard to read a long string of sentences and/or questions that are strung together with no rhyme or reason.
Put yourself in the position of the reader. I know that you know what you meant to say, but would some random stranger be able to read it and understand what you are talking about? If not, then edit your more to make your point clear.