First off I would not spend $400 on the TG Rock Assault housing. If you want a custom axle look at a diamond it is more money but you can have it build anyway you like, such as full floating with a 8.4 taco diff(strong). In short $400 is a lot of money to still have a V6 differential in your axle.
As for where to mount you spring and shackle hangers, it just depends where you want your axle to sit in relation to the body. I have my rear axle moved back from a stock location because I didn't want to cut the sheet metal by the rear doors to clear 37" MTRs. I would place your axle where you want it for your needs just make sure both sides are the same distance apart and it is square.
You might want to use springs other than trail gear, like marlin's springs. I would research the springs some people have had problems with them. You could also use Toyota junk yard springs if you want to save money.
If your 4runner is a daily driver I would recommend driving a rig that has a auto locker in it just so you know what you are getting into. Here is a review for a auto locker to give you an idea.
http://www.gentryoffroad.com/php/generalinformation/productreview/lockrite/
