First question is regarding pre-boil reading. Is this done prior to adding the extract or after as with extract brewing we never did this and the extract was usually added once the water came to a boil (We do full boils)?

Second Question: Top off water, after the complete mash out we had only 5 gallons. Our system requires 6.25 gallons for a full boil with 1.15 boil off. Should I be topping off the volume prior to the boil and before or after the extract add or should I be boiling everything and then topping off the primary to arrive at the 5 gallons?

Third question: If the pre-boil reading is lower than expected how do I know how much DME to add to get to the expected gravity, is there a general rule of thumb like 1lb per 5 points for example?

1a)

take your gravity when all liquid and grain is in the pot before the boil. First concept to understand in ppg (Points per Pound per Gallon). LME is generally 1.036. This means that in 5 gallons of beer post boil to achieve a 1.048 OG you would need:

48 OG X 5 gallons = 240 total points / 36ppg LME = 6.6 lbs of LME into the boil

Assuming that you start with 6.5 gallons of water before you boil, your pre-boil gravity would be:

240 points (from above) / 6.5 gallons = 37 or 1.037 OG

After the boil you will have concentrated the 1.037 into 1.048

1b)

Once this ppg concept is understood, adding grain is easier. Simply take the grains ppg and multiply it by your efficiency to get (most grain have a ppg that is also around 1.036) So if your efficiency is 50% then your ppg for your grain is:

36 ppg * 50% efficiency = 18 ppg

using the same example above, if you want all of your total gravity to come from grain (240 total points) then you'd use:

240 total points / 18 ppg Grain = 13.3 lbs of grain

It is pretty easy to rearrange this equation so that you can use OG, volume of water, and lbs of grain used to calculate efficiency (remember that your extract efficiency is always 100%)

2)

Either will work but if you can top off prior to boiling I think that is easier. I will sometimes take a gravity reading right before flameout and if I'm high on gravity I will add a bit of water to bring the gravity down. The boiling also sanitizes the water.

3)

refer to the ppg explanation above. DME's ppg is generally about 1.042. Following the above equation, if I have 5 gallons with OG that is 4 point to low (1.054 but looking of 1.058):

5 gallons * 4 OG (too low) = 20 points / 42 ppg DME = .47 lbs (about half a pound of DME)

in other words, half a pound of DME will raise the gravity of a 5 gallon batch by about 4 points.

Hope this helps