First All Grain Questions

I did my first all grain recipe yesterday. I brewed NB's Speckled Heifer kit and used BeerSmith 2 to come up with the
calculations. I hit the volumes and temperatures but I was consistently short on the gravity.

Let me back up and give you some background info. I used 5 gallon water coolers as my HLT and MLT and I had a 9 gallon brewpot.

BeerSmith told me to use the following water volumes for 8.5 lbs of grain;
Mash In 10.63 qt of water at 163.7 F, rest at 152.0 F for 60 min
Mash Out 6.80 qt of water at 202.2 F rest at 170.0 F for 10 min
Fly sparge with 3.43 gal water at 168.0 F

My preboil gravity was estimated to be 1.039 but measured at 1.030. That's a brewhouse efficiency of 63%.
The estimated OG was 1.045 but was actually 1.039.

I pitched the yeast and it's been really bubbling for 24 hours.

What could I have done to increase the efficiency? During the sacch rest, I simply put the lid on the cooler and left it alone for an hour.
Should I have stirred it occasionally?

How big of a deal is it to miss the gravities like this? Would extending the boil been the right thing to do?

There a few things to consider. Programs like beer smith and promash have settings that you need adjust for your particular set up. These settings are wort loss due to dead space, evaporation rate etc. These calculations will differ from rig to rig. Dialing in your brewhouse efficiency will take several batches, and will even differ from recipe to recipe because of type and amount of grain (more grain=less efficient). For example: If beer smith says 75% efficiency and you should have 5.5 gallons in the fermenter with an OG of 1.1050, but you got 1.045 here is what to look for.... Did you get 5.5 gallons in the fermenter? If you got six, the wort is watered down by the extra sparge water. When you took the temperature, did you take it in various locations? you would be surprised to find the top of the mash to be at 150 degrees, the middle at 148, and the bottom at 145. It happens. Did you recirculate the mash untill it ran clear before you sparged to ensure the grain bed was set? If not, the sparge water may have channeled the path of least resistance, leaving some sugar in the grain. Most rigs get about 75% efficiency, if you are lower than that, look at the program and your processes. It may be both.

Thanks for the reply. Beersmith said I should have had 5.5 gallons in the fermenter but I was just shy of 5. I didn't take temps in various locations mainly because my thermometer is short. I plan to get a longer thermometer to fix that.

I did recirculate the mash. When the sparge water got down to the grain bed, I noticed that it was not level. Instead it was like an island in the middle with a large channel around it. I wondered if that was an issue. Should I have done something to try and smooth out the grain bed?

This is your first AG, so 63% isn't really all that bad. When I first started doing AG, I kicked up the base malts in recipes by 10% to compensate for dialing in my process, and as you get better, you'll start to exceed the target gravity. That's when you start pulling the base malts back down in the recipes.

The island with the channel around it sounds like the mash is compacting. This happens when the transfer is being conducted too quickly, and the grain bed pulls away from the sides of the mash tun, allowing the fresh sparge water to run down the side of the vessel instead of through the grain, resulting in lower efficiency (sugars left in the grain). The sparge and transfer process should take 30-45 minutes, even up to an hour depending on your equipment. This sounds like a long time, but it allows the grains to remain in suspension, so the sparge water will travel through out the grain, bringing as much sugar as possible along with it. About efficiency inputs in brewing programs: The previous poster was correct, in that to adjust your gravity, add more base malts and corresponding specialty malts. One nice tip: Start to think of recipes in terms of percentages of the grain bill, instead of .5 lb of this and 1 lb of that. This allows you to make adjustments more easily, and you can compare contrast recipes much easier, because they will be in common terms.