I have been training seriously for 6 years for various goals - climbing, adventure racing, and fell running, basing some of my workouts on those shown at Gym Jones for the last 2. My training for distance has always been based along the lines of an aerobic base from long slow distance work, sharpened by a shorter period of intervals nearing the event - fairly standard practice.
Correct me if I am getting the wrong idea, but your workouts - particularly for cycling, seem to be primarily intervals, often placed in a longer (3-4hr) ride, but intervals nonetheless. I also notice your frequent use of a fixed gear bike, which is obviously an enforced interval workout. This type of training is obviously at odds with the "LSD for as long as possible do not go over LT etc etc..." crowd. It details a similar type of training in your book "Extreme Alpinism" (I know some of what you believe now is at odds with the book) beginning with power endurance and power, and only using extensive endurance at the end of the training cycle.
I am currently training for a 50 mile trail race in December. My current training is simply building up mileage on foot, with a longer run every 10 or so days, plus 3 or 4 circuits/strength/etc per week, plus whatever climbing I can do. I would be interested to know how you would integrate circuits/strength training more effectively into a running program, whether I should be perhaps developing power initially (coming from a decent level 400m sprint background (49.0s), I have a fairly large reserve of speed and strength) or simply going for mileage/time on my feet, and anything else I am completely missing and should have picked up.
I continue to read, take in, and learn from whatever you put out
I've been meaning to answer for a while but to do so is time-intensive and the other work takes precedent.
Low intensity volume followed by higher intensity work to improve specific characteristics (MVO2, LT, economy, etc) is still gospel IMO. But if you have been training consistently for six years, and improving over that time then "low intensity" now should be different than "low intensity" five years ago. So what does LSD mean today? And when is it appropriate to put in the volume, when and how often is it right to do the shorter, hard efforts? When is the time to mix different types of intervals into the longer efforts? Etc.
The problem with Ex Alp was the same we run into today if we try to write a one-size-fits-all training schedule. I took it as a given with the Ex Alp program that the volume work had already been done, or that the user had, at minimum, some level of aerobic base to work from. One reason the endurance focus came back at the end is because all of the hard, high intensity work prior would have favored glucose metabolism, which should not be, can not be the dominant contributor in any "long endurance" type of event. Besides, the Ex Alp progression was a linear periodization model wherein, by the time a climber went out the door to peak, his last real strength training effort would have been months before so peak force would have dropped off during the interim. Hence the admonition to train to be 120% stronger than necessary during the strength period (this implies knowing how strong is 'strong enough'). These days we are doing things differently enough that even though we follow a cyclic emphasis with our athletes a significant loss of strength (gained during the preparatory and strength phases) does not occur across the entire cycle.
If you are looking at my training for this season the glaring omission is the 100 hours of zone 1 intensity in the month of May while I was climbing in Alaska. That came on top of four months of mixed low intensity and interval work, preceded by general and specific strength phases beginning in November. Use of the fixed gear over the winter had more to do with developing the neurological capacity to spin at high cadence, as well as strength-endurance while standing. The interval nature of the tool wasn't the point. Besides, my cycling coach considers fixed gear efforts to be steady-state, and they are when compared to what actually happen in a cycling road race with violent accelerations followed by periods of relative calm.
Earlier in the summer (fresh back from AK) I used intervals, either on their own or mixed into longer duration efforts, to fill in the holes I found in my fitness. The two factors are LT, hence long-ish steady state efforts right around LT. And fractional utilization of VO2, meaning, while I have great 5-second to 5-minute power, at longer durations power drops off in a non-linear manner. My coach and I suspect that O2 demand overruns the supply side, or I am neurologically predisposed to lower intensity efforts and different joint mechanics, contraction times, posture, etc (from too much zone 1 intensity and too much time hiking uphill in May, which due to 25 years of 'memory' my body adapted to quite rapidly). The cure for both is high intensity intervals to boost aerobic threshold, i.e. VO2 Max, and to train the body to accept higher power output as normal, and a stimulus to better movement economy at race pace.
Even now, intervals tucked within longer ride play a significant role. And I'm doing different types throughout the year to address different issues.
Anyway, the order for building toward the 50-mile race should be general distance, hill work to develop specific leg strength and strength-endurance, aerobic work on the track (max VO2 training), then maybe a little anaerobic work though for an ultra this energy system won't see much use and may not need to be trained since doing so lengthens recovery time between workouts, and then a rest phase. If volume and intensity have been high one needs a drastic taper. For ultras people use anywhere from seven days to three weeks, depending on the event, and depending on how quickly they normally recover and restore themselves. The one thing I'd have changed in the 4-month program I used to prep a girl for the Wasatch 100 last year would have been to lengthen the taper, as eight days wasn't enough. But that's her. Generally, during the taper one should do a combination of aerobic and anaerobic work, high quality as well as low intensity, but with volume greatly reduced. Follow each high-intensity day with an easy day. There are plenty of articles on tapering on the web.
Load gym work into the program up front and gradually shift away. Cut it to 1-2 days per week about 6-8 weeks out from the race, depending on what you are doing and how you are recovering from it.
And for an ultra, you need to spend time on the feet beforehand. It takes time and miles for connective tissue, muscles, and brain to adapt to the impact, especially as hours pass and muscles become less elastic. Because you have a big speed reserve already you don't need to address speed specifically unless the terrain is very different from the track, i.e. a trail with significant altitude gain and loss. Then it would be good to do some downhill running on trail-type terrain just to build confidence and muscle memory and "looseness" so you can flow. Also, learn to "walk really fast" uphill because its smoother and with less jostling you may be able to eat and drink.
On the subject of speed, check out Matt Carpenter's story about the Leadville record here: http://www.skyrunner.com/story/2005lt100.htm It's eye-opening. But it must be said he didn't do that training in a vacuum. Years of prior work in different speed and endurance zones allowed it.