On further researching and a tip from my own personal fishing guru, I found this little device, which is exactly what I'm looking for. At $125 (the cheapest I've found it so far,) it is a pricey but brilliant solution. Its called the Fish Hawk TD and as it descends it takes temperature readings every 5 feet up to 300 feet. When you bring it back up it reads off starting at 0 feet at 5 foot (or meters if you choose metric readings) intervals. You can also use it to see how deep your line is running. Naturally I haven't actually used one but the reviews are excellent so I may take a chance and pick one up. Check out the little video on the web site - a very cool piece of hardware.
http://store-7f951.mybigcommerce.com.../fish-hawk-td/