If you take his pulse immediately after you stop trotting (before you cool him down), don't be alarmed if his heart rate is above 90 or even 100 bpm. Anything under around 150 keeps you in aerobic exercise, which is what you're going for (this is where a heart rate monitor is useful in conditioning for longer races - you can make sure you're keeping the heart rate at an aerobic level rather than moving into anaerobic (usually above 170 bpm), which can lead to problems if kept up for too long. This is why it's important to cool down, but not for too long, since you need them to come down within a reasonable time and still have an accurate measure of fatigue.
I found an excellent article where I got the bpm numbers and it's all about measuring fitness by heart rate and is featured on a site specifically for distance riders. I didn't read the whole thing, but definitely plan to since it looks like really good info! http://www.distanceriding.org/php/ar...ingFitness.pdf