Kinesiology / Biology Question

Details up front:

• Did 2 months of marathon training
• Ran marathon about 2 weeks ago
• Getting back into general physical preparedness training
• Perceived level of exertion is very skewed (started my interval workout today at what I thought was an 8 (out of 10) but by the end of the workout I realized it was closer to a 5)
• Recovery time is very good (heart rate and breathing were back to near-resting level in about half the pre-planned time, although this could be tied to my exertion level being lower than planned)

I have a pretty decent understanding of physical training (I've done a good amount of recreational research) but I'm looking for more details. I know my body adapts to the stresses I place on it, and adapted to distance performance, but what SPECIFICALLY was happening? Is it controlled in the mind? Either physically or physiologically, what changed?

Now for the long version:

I did 2 months of training for a marathon, and was very well prepared when I ran it (I am 5'11", 195 lbs and ran it in just under 3 hours!) I have since gone back to more short interval and crossfit type training since that is what I normally do.

I rowed collegiately and have an ergometer (C2 model C) and today I did my favorite workout: 5 x 1500m / 5 min rest. I wanted to do each interval at a perceived exertion level of 8 out of 10 and maintain negative splits. I thought I was throwing down pretty well on the first inverval, but found that I had fully recovered to resting heart rate and breathing within about 30 seconds, so clearly I wasn't working hard enough. I continued to negative split for each piece, but still took no longer to fully recover than 2 minutes, and that was after the final interval.

After the first inverval, I thought I was rowing at about an 8 out of 10, but by the time I was done, I realized I had probably started at closer to a 5 out of 10. My last interval was probably closer to 8 out of 10.

As stated above, I have a decent understanding of energy systems in the body, how distance training makes us more accustomed to generating power by burning larger amount of fat than glycogen and ATP, but how specifically does the body regulate what type of fuel is used and in what amount? What triggers the shift in saying "I have done this before and know I can maintain this level of exertion with x amount of fat and y amount of glycogen"? And finally, why has my recovery time improved so much?