Glad to see you're landing on a Heatmaster. Lot's of happy customers on this site!! As far as choosing which model, can you share what your insulation quality is like? One of the key differences in the 3,000 and the 5,000 is that the 5,000 comes with 2 sets of ports on the back of the stove. Scott7m on this site will really help you zero in on the appropriate sizing of the unit.
As far as E vs. the standard, I would recommend the E. The 2 most experienced Heatmaster dealers on this site say that there is quite an efficiency difference in the 3,000 and 5,000 E models over the standard. It becomes less noticeable in the 10,000 and 20,000. I went with the 10,000E and I'm glad I did. No, I can't compare it to a standard 10,000, but it makes me feel better in my mind. That extra by-pass makes sense to me. Is it worth another $1,000? I don't know. I can say that the $1,000 is obvious as far as construction goes. More material, more welds. It's not just a gimmick markup.
Will the standard do the job? Yes. Will you be wondering if you could be burning less wood when you stare at your stack on the standard model? That's the question you'll have to sleep on!!