Bike-specific shoes have been around for a long time. Basically, the cleats on your shoes clip into your pedals, allowing you to generate power throughout the pedal motion - not just on the down-stroke. Of course, if you're here, you probably already know that. The problem is that the position of your cleats are fixed, with only a small degree of adjustability.
A couple of years ago I read about some people toying around with a midfoot cleat position. Specifically Joe Friel, writer of the Cyclist's training Bible and Triathlete's training Bible, had a really good argument for midfoot cleats which made sense to me.
The idea is that moving your cleat to the middle of the foot effectively takes a lot of the strain off of your calf muscles, as your are decreasing the moment arm between your ankle and the pedal. This can potentially have a large impact on calf fatigue, which comes in play on particularly long days in the saddle, or especially during multisport (duathlon and triathlon) when you have to get off the bike and RUN a great distance.
Since I made the switch, I've done a 2000+ mi bicycle tour, and a very challenging Ironman race. Which I don't have hard data, in my opinion the new cleat position did improve my performance. It definitely didn't have any real drawbacks for me.
The only potential negatives I can see are:
This method will work best with shoes with flat, plastic soles. Carbon is OK, but you'll need to be careful about drilling. Shoes with non-flat bottoms are tricky. I'd suggest trying to fill in the holes to try and create a nice flat surface to work with. I have found a couple of models from Sidi have a nice flat bottom (mine are Sidi T2)
For cleats/pedals, I really like Egg Beaters. Dead simple, easy to use, and they allow for a lof of twisting (good on the knees for long distances). That being said, different cleats should work with this method, but becomes more difficult. With 3-hole cleats (like LOOK), for example, you will have a 3rd attachment point to plan for, and you'll want to make sure the cleat makes good contact with the shoe. Just something to consider.
As far as tools, all you need is a drill, tin snips, and whatever tool to drive in your cleat bolts.
Additionally, you will need 4 Tee Nuts (T nuts) and matching bolts. 1/4-20 size is very common and can be found anywhere. However, I found that with 1/4-20 size hardware, the bolts tend to loosen over time. Instead, I recommend looking for M5x0.8mm Tee Nuts. Harder to find, but will fit the cleat bolts you already own, plus the tighter pitch on the threads means that they are less likely to loosen over time. McMaster Carr has them, but only in pkgs of 100. I found some on eBay. Optionally, thread locker (such as Blue Loctite) can be used to help secure your bolts.