Got super stoked about this recipe by reading through the first few pages of the thread, and brewed a 5 gallon batch 2 days ago. Since then, I've read through ALL 41 PAGES of the thread, and uncovered all the issues with separation. Lucky me that I uncovered the issue before proceeding with the addition of root beer extract! I did a little digging, and found a recent Hard Root Beer recipe from BYO:
"Ingredients
4 lbs. (1.8 kg) pure cane sugar
1 tablespoon (15 mL) molasses
½ tsp. yeast nutrient
Root beer extract (quantities vary based on extract)
2-4 tsp. baking soda (added to taste)
Clean fermenting ale yeast (Champagne works well also)
2 lbs. (0.91 kg) sugar to backsweeten (added to cold keg)
Step by step
Bring sugar, molasses, and water to a boil for 15 minutes. At flame out add yeast nutrient. Once cooled to yeast pitching temperature, add the yeast and allow the temperature to rise naturally to the upper limit of the yeasts range; you want a good and fast ferment. After 10 days, cool to near-freezing to drop out as much yeast you can. Transfer the clear finished beer into an empty corny keg and add in the root beer extract and baking soda to taste. Finally, add the sugar (dissolved in 1 qt./1 L boiling water) to backsweeten. Mix all this very well or the dense sugar syrup will drop to the bottom and make for an awkward first pint.This beer likes to be well carbonated try 2.4-2.7 volumes and will stay good for quite a while in a kegerator."
A couple of things stand out to me here. First, the primary is allowed to go for 10 days. Second, they recommend cold-crashing the beer to near-freezing to precipitate out as much yeast and other solids as possible. Third, they recommend baking soda to reduce acidity. I'm going to try employing all of these techniques to my batch which is roughly based on the original recipe, and I'll keep you posted.