If you brewed the recipe on the Mr. Beer site, it's got 2 x 1.2# of malt extract for a total of 2.4# malt extract for 2+ gallons of beer. That's not bad (especially compared to the single can & booster original recipe), but it's still not exactly what I would call full-bodied. The apple smell is probably a by-product of the fermented brown sugar (1 cup, right?) combined with warm fermentation temperatures. For a full-bodied beer (without being really heavy), try 3 lbs. of malt extract (syrup or dried) and an ounce of medium bitterness hops (e.g. Mt. Hood - 1/2 oz. boil 45 min, 1/4 oz. boil 10 min, 1/4 oz. end of boil) and a package of Cooper's Ale Yeast. Forget the brown sugar until you've made something you like. Keep in mind that they hopped the can of brown ale to balance out just that can of malt. With the addition of the second can of unhopped extract, you skew the flavor toward the malty/sweet side. IMHO, a half an ounce of some medium bitterness hops would help balance out that sweetness, plus it would help mask the flavor of the fermented brown sugar. Frankly, if you will give the beer another month or so in the bottle, it will probably lose a lot of that funkiness. Hope this helps.
Scott Birdwell
DeFalco's Home Wine & Beer Supplies
Houston TX