i wouldn't trust anything clone brews says. you can make some good beer with their recipes, but it'll never be on mark with what you're trying to clone. it's more a "learn the style" book.
volume is key, too. pour 1 gallon at a time into your fermentation vessel and make marks all the way. i make a 5.25 and 5.5 gallon mark, too. that way, i can always be spot on with my gravity and if i need to add water to drop it, i can.
and yeah, mix the s*** out of it before you take a sample.
and no, you will CAN NOT miss your OG range if you have the correct volume and the correct amount of sugars/extracts. the only thing that could be wrong is your recipe specifications, unless a mistake was made in the process.
