Here's a link on centering a stk Fj40 rearend.
Windshield/Glass Installation - Land Cruiser Tech from IH8MUD.com
www.ih8mud.com
I did this same thing to my 40 rear end probably 15yrs ago when I went to a center rear output T/case. It allowed me to use my 3rd member which had 4.88 gears and a Detroit locker in it, It also eliminates the C clips that hold the 40 axles in. Another plus is both mini truck axles are the same length. I'm pretty sure you can do this with the FJ60 axles using a Tacoma rearend. The job was not that difficult.
Back in the 80's & 90's all my friends I wheel with have jeeps. Later 76 to 80 model CJ's had 2 piece rear axles in their model 20 rear. The axles were really weak and the hub would spin. The standard upgrade was to install an alloy axle kit made by Moser. When the 90's jeep YJ came out, the easiest way to get it ready to trail ride was to add a 4" lift and run 33 or 35" tires, add a lockrite and install Moser alloy axles in the Dana 35. The Dana 35's axles were really weak and C clipped and worthless with larger tires. Back b4 longfields, and short lived marfields, I was breaking stk birfileds when I had a lockrite in the frt. So, I had Moser narrow the long side of jeep waggy dana 44 frt end for my 40 which worked well . They also cut and resplined several full size truck dana 44 axles to fit the housing. A couple of times, I would stop at Moser on my way to FT Wayne, IN. and drop off axles to get cut and splined in the AM and I would pick them up later that day. I've always had good experiences with them