I currently ride with Specialized Sport mountain shoes, and I have the Shimano m520 on one bike and m540 on the other.

Between the Specialized Sport and Comp, get the Comp. It's worth it to have the ratcheting buckle instead of all-velcro. Being able to reach down and tighten the ratchet while riding is worth it. I'm sick of only having Velcro straps, and I am currently shopping for new shoes to remedy this situation.

That said, neither shoe is very stiff at all. That's another reason I'm currently shoe-shopping, I feel like the flex is bothering me and causing some hotspot/toe numbness. Compare them to the more expensive mountain shoes or to the Specialized road shoes, the Sport shoe isn't as stiff.

Between the m520 and m540 pedals, the 540 looks a lot cooler and isn't much more expensive. Functionally, I can't really tell them apart on my 2 bikes while riding. I've read the 540 will be more durable, and I'd believe that from looking at it and the "feel" of it, but I think either one will serve you well.