I like your 9" idea, and, had I not gotten a deal on a hp44 and dana 60 with the right gears, that was the path I was on. The 9" has the advantage of being super-super cheap to build because they're as ubiquitous as a SBC. One thing you might consider, should go centered rear, is looking at NASCAR full-float 9" rear axles. Their advantage is 1) they are usually 1/2 the price of a comparable fab'd housing, 2) they have all the best parts inside, and 3) you can get detroit lockers are part of the deal... seriously, they're ~$1200 to buy. Given you're close enough to NASCAR's stomping grounds (at least a whole lot closer than I), they're a good option.
In 4x4s, there's fact, opinion, and trolls (fact - you have a FJ40, opinion - how they built theirs, trolls - how they want to spend your money to build their vehicle)... be sure you learn to identify which is which before you spend your hard-earned money.
I like the 9" because they are a light assembly, but they are a fabricated assembly which is thinner and less robust than a cast housing with pressed-in tubes. CV joints are fine for what you're doing, but, like anything else, are almost a preference rather than a necessity... not to mention, they're about 5x more expensive to rebuild than a broken u-joint. Since you're already talking wider wheelbase and custom axles - you lost me as to the reason why you'd use spacers.... if you're going to 4 link the suspension, the more axle tube you can get the happier life will be for you....
doublers, with the stock wheelbase, you will be challenged to get enough driveshaft length.... and I'm not sure why you'd need a doubler with this DD-style build. the low 1st gear of the 4L60e with 33" tires and you'll be just peachy in the world... I'd run 4.11 gears as you folks don't have the mountains we climb in the west.
Dana 300s are a whole lot cheaper to buy and build than an Atlas, but the moment you start building a dana 300 - the atlas can be a reasonable priced alternative. With that said, I have a dana 300 in my '40 - and the all-in cost for a 32 spline output, 4:1 gears, rebuild kit, purchase of the case and adapter is $1700. A bare Atlas 2 is $2600 then you need to buy the adapter and shifter. The Atlas is a lot prettier, though, with that cute billet case (okay, perhaps I just moved to troll... sue me)
Offset pumpkin... an advantage of centered differentials is the ability to only need one axle as stock in case of breakage; another advantage is related to length and how that relates to stress... until you're in the 38" tire range... don't worry about it.
