This is the biggest red flag I’d focus on addressing. Aside from that, below is my view.
I’m typically a XCO racer (1 hour - 1:40 min races) but like to do a 100 mile MTB each year. Last year I did the Lumberjack 100, which had 10,000 feet of climbing (90% singletrack) which took me just over 9 hours to complete. This year I have the Marji Gesick with 12,000 feet of climbing (expecting a 12-14 hour event). I only did 2 rides over 3 hours to test nutrition and fueling strategy last year and don’t plan to do more than a couple “big” rides this year either. Mainly because it’s not needed and the recovery from those rides disrupts my training. Those big rides help test nutrition/hydration and get your mind prepared for the efforts, but the training for those efforts can certainly be accomplished by 2 hour trainer rides. Remember, 2 hours of constantly pedaling on the trainer easily equals 3-4 hours outdoors. Outdoor rides have lots of micro breaks that you just don’t get on the relentlessness of the trainer. I’m not so sure about “muscle memory” from long rides, but maybe mental memory of being able to suffer is what is gained. However, for me those long rides are such a big mental drain that it almost does more harm than help. Unless your pace is below race pace but then I’d question its usefulness. What works at sub-race pace MAY not work at higher and longer intensities.
I’m going to disagree with a few point from others suggested above, though their advice is sound in general. I’ll just address the points where my opinion differs from others.
First, if your race is mostly singletrack (unlike Leadville which is more of a gravel race), than I would recommend General Build. Unless you have numerous big fire road climbs over 30 minutes, Sustained Build will not prepare you for a MTB Ultra. I used to think this as well, until I put a power meter on my MTB. Of course this is location and course dependent, so look at the event profile. In Michigan for example, everything is punchy and no climbs are typically over 10-15 minutes. All the singletrack climbs require punchy efforts then back to z2-3 riding and plenty of z1 and coasting. Often little (less than 10%) of effort is found in that sustained effort of sweet spot and threshold. Typically you either need power, lots of it, or you’re at your all day pace. This is what General Build prepares you for and has an amazing blend of both. My recommendation is SSB 1 &2, General Build then Cross Country Marathon (unless your “MTB” race is really a gravel race with some single track thrown in).
Low volume plans MAY be your issue as it’s just not enough proper stress to prepare you, but it’s just as likely to be a fault of pacing and/or nutrition/hydration strategy. Instead of doing LV and adding rides to your plan, I’d recommend doing mid volume and substituting outdoor rides for planned workouts. This way you can see what the TSS progression is intended and attempt to mimic indoor workouts outside, which is much easier now with TR offering outdoor alternatives. Also, once out of the base phase, I’d recommend doing your longer rides (2-3 hours) on singletrack if that is what your event will mainly be. The closer you are to your event the more you need to specialize with your outdoor rides to your event demands. Analyzing my long singletrack rides I’ve found it is near impossible to just ride z2 or anything sustained. I may be doing 150 watts during a trail ride then a section of trail forces me to do over 400 watts for 20-30 seconds in Eagle gear up and over a climb with roots and/or rocks. It is so difficult to do sustained efforts on true singletrack which is why I don’t recommend a sustained TR plan.
I’m not so sure your road group rides are doing you much benefit specifically for your event. Unless you’re pulling in the front and actually getting a proper structured workout in, these tend to be traditional base type mileage. Without seeing a power profile though, it’s hard to draw any conclusions. I’d just make sure your outdoor rides are accomplishing your intended goals.
Lastly, get to the bottom of your history of cramping issues. This is much easier said than done, but start experimenting with different products and strategies. Personally, I’ve found great success with Hammer products and follow their nutrition and hydration recommendations precisely. They have a free book that discusses how, when and what to do for events lasting 1 hour to 24 hours in great detail. I follow that religiously and have had no issues.
Good luck and get to the bottom of your limiters, I just don’t think the 2 hour training rides is one of them.