The main problem with using Fire & Fury for smaller battles is that a couple of extreme pairs of rolls on the Charge Combat Table can decide the game. Our usual correction for this is to use 8-sided dice for Charge Combats in smaller battles. You need a situation with at least 8-10 brigades on each side for a good game of F&F, although it is possible to scale up Johnny Reb scenarios by 'promoting everybody one rank' - replacing regiments with brigades, etc. The Fire & Fury rulebook is not easy to use in play - the binding is very fragile, and is necessary to pour over lots of verbiage to find something in the middle of a battle. It's possible to put all the essential rules on six typewritten pages - we use these 'reference sheets' that I've made up, during games, almost exclusively.
The 'Second Day at Gettysburg - Battle for the Round Tops' scenario is seriously unbalanced in favor of the Union, because of the 'perfect intelligence' factor. Gen. Meade knows what Rebel units are available, and if Lee commits all his troops, the Union can mass artillery on Cemetary Ridge, stage a 'Pickett's Charge in Reverse' and smash the Confederate center. Some form of unknown Rebel unit arrival and off-board reserve movement is necessary.