90 minutes is how long your glycogen stores last.
So, as you've noted, the key is fuelling in long races.
Pre loading is one aspect but also eating more during the race. from your account it sounds like you only took a couple of gels, 3 maybe? I'd be eating much more than that - for example 3-Peaks cyclocross, which is 3 and a half hours, I consumed a litre of Coke and 6 gels, and maybe should have had more.
Interesting thing with cycling is that because you don't trash your legs like you do running you get much more of a sense of how fuelling affects your performance, basically as long as you keep fuelling well, you can keep going strong.
With running you batter your legs and put the fatigue down to that - but whilst part of it is the battering a big part of it must also be fuelling, but the battering masks it somewhat.
However the bumping up and down of the stomach you get running compared to cycling (even the 3pcx which will be bumpier than most) can make eating (or managing the gut's reaction to fueling before and during) harder to guage/learn
Jelly babies - 2 every 15 minutes. Worked on the Highland Cross and Great Wilderness Challenge:-)