I don't think I've ever heard of anyone doing this, even back to the original game. Doesn't mean that it didn't happen, but just that it never even occurred to me that someone would do the trench run without the Mako.
If all you have is your autosave, and you're on foot, then I doubt that there's anything that will help in terms of reloads or whatever. If you're not averse to using console commands, you might try the SpawnVehicle command. That should spawn a Mako at your location. You could also try temporarily giving yourself unlimited Storm time and using the SetRunSpeed to give yourself super speed, although I don't know if you'll be able to set it high enough to make the run in time.