These are great questions, and I’ll try to cover them all as best as possible.
To begin, muscular endurance training can form a part of many different modalities and depending on your sport of choice, and it is present at various stages throughout the macrocycle. In the case of mountain running, the first thing we should think about is how specific the ME training is to the sport, and therefore look to make the training look increasingly more like mountain running as you get closer to your goal.
Ok, with that in mind… we tend to advocate the gym ME first (for runners) because it is a localized workout: the load placed on the muscle groups in that workout is much more targeted than an uphill running session, and furthermore it reduces the global fatigue effect on the body. In other words, you can do a good job of hammering on the local muscles (such as the glutes/hamstrings, and quads) in the gym ME without a huge aerobic load and resultant full-body fatigue. In this way, the gym ME can be inserted earlier into the training progression with less concern that it will demand significant recovery and hamper overall volume.
Uphill ME vs. Zone 3 vs. weighted uphill: leaving the gym, there are several different ways in which you can get focused ME outside. You can do short, bounding/explosive repeats uphill with weight, or longer zone 3-level uphill efforts without weight. Or, you can do heavily-laden long, sustained steep climbs. So which to choose? Again, refer to the specificity argument – what are you trying to train? Generally speaking I put athletes on a progression of gym ME, then moving to Z3 uphill intervals (unweighted). The reason is because I want to first improve local muscular endurance via the gym session, then I want to engender greater economy in those muscles (i.e. increase speed) by challenging them to run uphill for longer durations and sustain the fatigue onset. This is the effect of the Z3 intervals. The uphill weighted sprints/bounds have a more proximate effect to the gym ME, in that they tend to be more localized and less global (because the duration is shorter, explosiveness is higher, and due to the added weight), so they can be a good choice if the athlete needs to improve their force production before going to longer, more global and specific intervals.
You can potentially do both the gym ME and uphill Z3 workouts in the same week. One is localized, one is global, so provided your base capacity is strong and you’re recovering well between sessions, they complement one another well. At a certain proximity to your goal event it’s important to move on from the gym ME to something more specific – maybe keep the uphill Z3 intervals and add a progressive distance workout, so that now you have two specific sessions amidst your maintenance volume. We’ve found that tapering off the gym ME for several weeks is really valuable for netting the benefits of it prior to an event.
Adding reps instead of using weight with the gym ME could be problematic because you risk increasing the global load without a comparable gain in local muscle effect. Finding weight shouldn’t be too hard, provided you’ve got some rocks/books/small children around. Scott used to make me do these jumps with him sitting on my shoulders, so you can certainly employ some creativity…
Finally, to your question on whether using the uphill weighted sessions for ultra running is more beneficial. The reason we use that workout a lot with mountaineers and climbers is because their rate of climb and foot cadence is much lower on average than even a 100-mile runner. As such, you can afford to increase the load and target ME that way without fear of reducing economy gains. For the runner this can be detrimental. Even at an ultra-shuffle, the runner’s cadence and pace is higher and it’s important to think about the need for that economy throughout the training process. Using uphill Z3 running intervals is a great way not only to improve muscular endurance, but also to improve neuromuscular efficiency with cadence on steeper terrain. Think of it as training a margin of speed and economy above what you expect to be using in your event – it’s always good to have that buffer, regardless of how deep you need to tap into it. Again – always think about specificity and what the optimal movement rate is for your sport.
Whew! How’s that for a long-winded answer?