The short answer is we don't know the timeline exactly, but I can think of plenty of plausible ways he could have walked to the trucks site.
First of all, we don't really know how far away the trucks got from wherever he was shot. They may have taken a detour, they may have been stationary for a while, they may have had to take a windy route due to lack of roads, etc. Maybe the site he was shot at is only 10 miles from the nearest highway through the desert, but takes an hour of windy dirt roads to get to by car.
Second of all, we don't know how long after the massacre he woke up. For all we know he woke up long before the massacre occurred. All we know is that the sun is up. But we can't say for certain that the sequence of events didn't overlap.
I can agree that it seems a bit super-human for him to have survived at all and then catch up with them, but that is also part of the characterization of the Sicario. He's a survivor. We're meant to suspend our belief a bit and accept that he was able to walk that far out of a sheer will to survive.
Bottom line is we don't really know how far he walked or how long it took him, but that's not really important to the story.