I've been running five days a week for the last six weeks to prepare myself for a couple of mud runs that I plan on participating in later this summer. I'm doing c25k on Monday, Wednesday and Friday (just finished week six), sprint intervals on Saturday and a long slow distance run on Sunday. In that time, I've seen an incredible change in my ability to recover from even the most difficult workouts, but my endurance seems more or less the same. Shouldn't they be improving at roughly the same rate? Is there something about my routine that's causing my ability to recovery to increase faster than my endurance?
I'm still fairly new to running and working out in general, so nothing scientific or exact. Just basing it on how I felt when I first started running a few weeks ago versus now. Is there a better way for me to be measuring it?
Well how exactly did you feel? 
To me it's an indication that you've developed adequate capacity, but need you need to develop aerobic stamina/power now. Start slowly and gradually by substituting a single day of lsd, for running at your AT anaerobic threshold (roughly 75-85% MHR) that's where power is created.
When people, particularly those that have been doing lots of slow steady work and aren't yet prepared to work at AT (not fun) for a steady pace, begin I like to introduce them to it thru Fartlek style running - 15-30 minutes of "zone" @ 70-85% until you can do this for 30 minutes, then I switch to a 15-30 minute continuous tempo run at AT. There's lots of swearing, but it's so damn effective. when you've adapted, add another day etc. etc. You'll see your race pace increase.
^^^ Listen to this man.
For me a good guideline is how quickly my HR drops when doing sets of 5 minute intervals. If it takes longer than 60 seconds for my HR to drop from 180 to 110, then I'm in not in great shape, or that I went way too hard in the interval for my current condition.
I run on a treadmill and generally do the same pace for each workout, so I'm not sure if I'm any faster but I can run longer than I did when I started a few weeks ago. I know that my recovery is better because I'm usually ready to go again fairly soon after a run and active recovery isn't as big of an issue as it used to be. Basically the best piece of advice for me is to get a heart rate monitor, learn my limits and go from there?
Leigh - A heart rate monitor is invaluable. Training without one is like lifting weights without the numbers on the side
For running, swimming and biking, I absolutely disagree.
Running you can do very well on perceived exertion. For speedwork you are almost certainly on a track, so you can very precisely figure out your speed and therefore effort level. Whenever I've trained with national or world class runners, the only people who showed up to workouts with HR monitors were triathletes.
Swimming never saw anybody but slow ass triathletes using a HR monitor. Just like running, you get good at gauging your intensity and you have the clock to tell you your pace.
For biking, HR is ok, but there is something way better- power. Your wattage is the best possible measure of how much work you are doing. Not cardiac output, but measuring cardiac output non-invasively... yeah.
I used a heart rate monitor to get a better grasp on my perceived exertion.