I just followed the suggestions at the Heartfixer page (which is basically the Cliff Notes of Yasko's program). I hit it with everything suggested, that I could tolerate.
http://www.heartfixer.com/AMRI-Nutrigenomics.htm
I can't afford Yasko's actual supps, so I checked out her supps and ordered exactly the same things in the same form, but in different brands from iHerb. It cut the cost in half.
I did order her CBS RNA, but it didn't muscle test well, so that I was able to return because you don't need to open the bottle to muscle test supplements.
As far as diet, I followed the free thiol diet and supplement list, instead of the low sulfur diet.
http://www.livingnetwork.co.za/chelationnetwork/food/high-sulfur-sulphur-food-list/. It's not as strict as the low sulfur diet, and it's still effective.
I still need to eat meat for various reasons, so I didn't cut back on that.
I started each supplement one at time. I did notice a bit of an increase in energy with the l-carnitine fumarate, and the Yasko multi (due to the TMG in it), so those were pleasant surprises. Once I got about a month into it, I noticed increased rotten egg/sulfur smell in stools. It's pretty noticeable - lol. I believe this can be taken as evidence that you're actually detoxing the sulfur and ammonia (even if the numbers on the strip stay the same).
To answer your question, I don't think there was any one thing, it was the combination of several things. I just wanted to get through this as fast as possible because you can't really crank on the B12 and methylfolate until you get this taken care of, and those are the meat of the program.
My ability for tolerating methylB12 is slowly expanding - from 0.5mcg to 1.5mcg. Yes, you read that right - when I first started, anything over 1/2 microgram caused excitoxicity. My goal is to get up to at least 1000mcg. I have SNPs that allow large amounts of methyl groups.