Stock Offset FJ40 cruiser rear end width WTW (Wheel To Wheel)= 1400mm=55.1” (inches)
Source: http://www.off-road.com/tlc/faq/frame.html#HD_NM_3
I have not measured the WTW myself but this should be pretty close

35 spline Dana 60 (semi-floating).
Also, you could make a 35 spline Dana 60 (semi-floating). The housing ends are about $65 a pair from Art Morrison or Dutchman or Moser. The bearings would probably be about the same, if not less. The axles cost about $400 but are probably the last and only ones you'll ever have to buy for that rear end (Dutchman has 40 spline Dana 60 axles with bearings, retainer plates, and studs for $470).

6 lug semi-floating 30 spline Dana 60 (55” or 58” WTW)
You could do the 6 lug semi floating Dana 60 using Toyota pickup axles, brakes, and a portion of the toy tubes with a Dana 60 center section and tubes. The width depends on the year of the rear end; 55 inches wide for pre-IFS rear ends and 58 inches wide for IFS truck rear ends.

The pre-IFS rear ends have 2 5/8” tube diameters so they will fit inside the 3.125” OD 0.313” wall tubes of the rear Dana 60 with a little grinding.

The IFS rear ends have much larger 2 15/16” tubes which neck down to approximately 2 5/8” near the housing ends. A good way to adapt the tubes together is to machine an adapter tube to fit inside both of the tubes.

Custom centered cruiser housing (55” or 58” WTW)
Custom centered cruiser housing ($350-400) using toy pickup axles and brakes. A guy in Oregon makes these housings. I think the guy is John Groves of Cruiser Parts in Grants Pass Oregon. Phone is (541) 479-5500.

Stock centered cruiser housing (1958-1962) (53” WTW)
Also, I can't forget the stock centered cruiser housing. Drawbacks: hard to find, uses 10 spline axles, and is 2 inches narrower than offset cruiser rear ends.

V-6 or turbo toy pickup rear end (58” or 55” WTW)
You could just use a v-6 or turbo toy pickup rear end. The toy pinions are the same size as the cruiser’s at the splines. Also, the axles are the same at the splines except they do not use c-clips. I heard that both (maybe only one of them…can’t remember exactly) the V-6 and the turbo toy pickup rear ends have stronger third members than the standard 4 cyl rear ends. They have a stronger 4-pin design carrier.

One last thing about cruiser pinions vs pickup pinions...the pinion splines and diameter of the splined part of the pinion are the same (fine spline ones). I know this because I'm using a pickup flange on my cruiser third member so I can use the Toyota pickup driveline which has a longer slip yoke. Also, the toy and the cruiser use the same pinion seal. The rest of the pinion is different.

Cruiser/toy pinion=1.107” diameter with 27 splines
Dana 44 pinion =1.144” diameter with 26 splines

9 inch rear end: ‘66-‘77 Bronco (58” WTW)
A 9 inch rear out of a 66-77 bronco would fit, although it would be about 3 inches wider than the stock rear end. These are 28 spline so new 6 lug 31 spline axles would be in order.

9 inch rear end: late 70’s Lincoln Versailles.
You could use a 9 inch rear end out of a late 70s Lincoln Versailles. It is approximately the right width. They are hard to find, use 28 spline instead of 31 spline axles, and are 5 lug (you could have the pattern changed or get new 31 spline axles with the correct bolt pattern).

Dana 44: Scout or Scout II
A rear end out of an International Scout or Scout II would work. They may be a bit wide though (4-6 inches?). I was told that a rear end out of an 800 series scout would be approximately the right width.

Dana 44 or solid axle AMC 20: Wagoneer (58” WTW)
Another rear end you could use would be a Dana 44 out of a Wagoneer or a solid axle (not the splined hub type) AMC 20 out of a Wagoneer. However, it is difficult to find the centered AMC 20 that has solid axles.

Dana 44: CJ (51” WTW)
Another rear end you could use would be a flanged axle Dana 44 out of an early to mid 70s jeep cj. Unfortunately, they are a few inches narrower than the stock cruiser rear end which results in a lot more tire rubbing in the fender wells. They also are 5 lug instead of 6 lug. To remedy these problems, expensive 2”-3” wheel spacers which adapt 5 lug to 6 lug could be used.

Summary:

The centered diff rear end that you choose to replace your offset cruiser diff is probably going to be a matter of $$$ in most cases. If you want the ultimate in strength then go with the semi floating 35 spline dana 60. The hybrid toy/dana 60 rear ends will work fine with moderate horsepower and will probably cost less than the 35 spline Dana 60. The Ford 9 inch rearends are okay if you have 31 spline axles. I wouldn’t use one if it had 28 spline. Also, I’ve seen the pinion support crack when they were used in friends jeeps.

The dana 44 isn’t much (if any) of an upgrade. The pinion is basically the same size and so are the axles. The only reason someone may swap it in is because it was the cheapest way to go for a centered diff.