Spring over axle is exactly what it says. Unbolt the axle from the springs. Put the axle under the springs. Bolt it back together with everything the other way up. You will have to weld a pait of plats of some sort to the axle to give the spring a flat serface to sit against. If you look at the mounting as it is you'll see what I mean. A couple of problems. You will probably have to lengthen the break lines. And the shock absorber may need re-mounting, as the plate it bolts to at the axle end will be about 2 inches higher after the conversion. Once it's done keep tightening everything up regularly for a while as the axle 'settles'.
Longer shakles will work. If you don't fabricat longer spring hanggers for the other end of the spring then you only get half the lift. Ie a 2 inch longer shackel will only give 1 inch of lift. Also longer shackles can couse less stability as they flex more from side to side. Fabricating lower mounting points for both ends of the springs negates that problem, but is more work. Any suspention lift puts more strain on the drive chain as props (and in the case of shackle only lifts, diffs) are put into angles they were not designed to work at.
A body lift can be used. Unbolt the body from the chassis. Lift the body up. Insert spacers of your required lift hight. Bolt it back together with longer bolts. This leaves all the running gear at factory spec geomitary, and keeps the center of gravity lower as the engine, gearbox and chassis are not being lifted. This has it's own problems though. Breack pipes may need lengthening. Stearing likage to stearing box may need lengthening. Gear lever can become awcward to use.
With all these lifts, if you go up, you need to go out (wheel wise). Wether that be axle spacers, wider dished wheels. Both!!! All the extral width and hight makes you car harder to get through that little gap your mate just spead through in his SJ. And the wider you make the axles the more strain you are putting on swivel barings, wheel barings, stearing components and suspention.
Personally I would not lift it. Just put as bigger wheels on as you can without fouling the wheel arches. Or as it's an off road only car, cut the wheel arches out to fit the wheels you want. Makes for a more stable, compact vehicle. And all the suspension geomitary stays where some little Japanies gentlman spent monthes desiding it shoud be.

Any veiws expresed in this thread by me are purely from my own experience, and (sometimes) falible memory. Hope my comments help, but please don't take them as gospel.