Here is another experiment you may be interested in: http://www.woodlandbrew.com/2013/02/rehydrating-safbrew-yeast.html
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Others might beg to differ, but in my experience...This has been my experience as well. 60 minute or 90 minute seems to provide the same conversion efficiency for the most part. To get a more fermentable mash, low temperatures and (perhaps to a lesser degree) long times seem to help.
Mash temperature has negligible effect on efficiency. Ditto for mash time. Ditto for water to grain ratio (i.e., qts/lb). If you mash in some water at 148 to 154 F for 40+ minutes, you're going to make beer at an efficiency that is mostly affected only by the extent of the crush. Beyond the crush, very little matters.
My experience. YMMV... but I doubt it.
How are you checking yeast health? From what I've read, the methylene blue stain is not accurate below 95% viability.I've read that too. It is "not accurate" to some level. Even the American Society of Brewing Chemists calls it not accurate.