I use Beer Smith to formulate my recipes and record the results. I also keep a physical brew log, just in case the digital one goes wonky... Still, Brew Smith is one of the best $21 I've spent for brewing.
I would suggest finding out what the gap for the mill at the LHBS is set to before you get any more grain from them. Farmhouse Brewing Supply mills their grain to .039". Try getting your next batch of grains from them to compare.
I would make sure you're getting all the clumps out of the mash too. I had one mash where I wasn't able to do that and my efficiency was pitiful (just slighly lower than yours)... I haven't let that happen again.
You can also try going with 1.5qt/# and see how that works.
I do like Beer Smith for helping to figure out the water volumes you'll need, as well as what temp to heat the mash water to. Keep in mind, you can alter parameters, such as how much water to grain for the mash, the temperature the grain is, the mash tun temperature (do you pre-heat it?) etc...
For reference, I used grains from FhBS for my Irish Red ale... Used 11# of grain, total, and had an OG of 1.064. The FG was 1.018, because I mashed at 154F. Next time I make it, I'll mash a bit lower.
I brewed a 10 gallon batch on the 2/26 with my brew-buddy... With 26.5# of grain, we got an OG of 1.065 (~10.5 gallons into fermenters)...
I made a partial mash old ale that had just over 11# of grain, plus 3# of DME, with an OG of 1.089... When I make that as an all grain version, I plan to use only end up using about 17-18# of grain to get an OG in the 1.085-1.090 range. I'm not planning on making that anytime soon, since I'll want to get my new MLT dialed-in first...
How many batches have you used that MLT/cooler for?