As someone who has battled efficiency issues, I would start with making sure your measurements are completely accurate before looking at other things (crush, pH, water chemistry, etc.)
1) is your thermometer accurate? If so, are you sure?
2) is your method of measuring volume accurate? If so, are you sure?
(are you relying on Ale Pail markings? They are notoriously inaccurate)
3) is your device for measuring gravity calibrated, and are you using it correctly? Are you temperature correcting if you need to?
The reason I say this is because I noticed the "~5 gallons" and "about 3.5 gallons" in your original post which to me implies you may not be measuring accurately.
Once I started measuring everything accurately, it turns out my efficiency has been spot on at ~77%, even though I was getting anywhere from 54% to 80% when I wasn't measuring accurately.
Also I'm being nit-picky, but you say "fermentation" several times when you actually mean "mash"