I'm not a doctor, but I know people who are doctors.
Seriously, do you have a wide forefoot? I do, I've found that Carnac Tri shoes are not good for me (numb toes) although the Ellipse was acceptable. I have since settled on shimano shoes, I have yet to try their tri shoe.
Which toes are going numb? Is it just your toes, or also other areas of the foot? If you can isolate the problem as specifically as possible, you will probably find the solution. This is probably caused by too much pressure on the nerves in your foot, but may be something else.
Check out this link, might be helpful: http://www.apma.org/sports/cycling.html
PS. I read Tom D's shoe fit guide, I'm not sure if I agree with his recommendations. I think cycling shoes should be snug, with no movement, but not tight, certainly not 2 full sizes smaller than my running shoes. But maybe he buys running shoes differently than me, I like them snug as well. Be willing to try different brands, and stick to whatever works when you do find the right match. But he's the expert, not me.