There's no real "stages" to upgrading any engine... but things do kind of lump together.
If I had to lump 1JZ upgrades into stages I would probably put them like this...
Stage 1: Walbro fuel pump, 2.5" IC pipes, medium FMIC (sized for ~400hp), 3" turbo-back exhaust, boost gauge, 3" pre-turbo intake tube with pod filter. Estimated 12-14psi of boost (due to boost creep).
Stage 1 estimated crank HP: 330-350
Stage 2: Stage 1 mods, 440 (or larger) fuel injectors, SAFC (or some type of fuel control), electronic boost controller (set to 15psi), upgraded exhaust y-pipe. Estimated crank HP: 360-380
Stage 3: Stage 1&2 mods, 550 (or larger) fuel injectors, 3" intercooler piping, larger FMIC (sized for ~500hp), 3.5" exhaust, boost set to 16-18psi (walking on thin ice with stock twins here), aftermarket cams, race gas/E85 OR water/methanol injection probably required at this point to prevent detonation (especially with the small stock twins cranked this high). If you plan to stop here, a good option at this point is fitting up a set of USDM JZA80 twin turbo's. They require some work to fit, but flow more and heat the air up less. Estimated crank HP: 400-450.
Stage 4+: Single turbo... this can get crazy, so the supporting mods will depend on what turbo you choose.
This doesn't include supporting mods that should also be done to support an engine making more power such as an upgraded radiator, external oil cooler, an upgraded clutch, 12v fuel pump mod or upgraded brakes. Also... I didn't really write this as an ideal way to gradually upgrade a car. It's best to figure out where you want to end up and build for that goal... It would make more sense to skip right to a big FMIC, 3" IC piping and 3.5"/4" exhaust if you ever plan to go above 400hp. No point in buying things twice. It's not ideal to have an intercooler that's rated for 700hp and 3" IC piping if your car will only ever make 350hp though (both will increase lag and the bigger FMIC will block the radiator more), that's the only reason I did it like this. Similarly, there's no point in having a 4" exhaust on a 350hp car, you won't gain much power on a 350hp car by going from 3" to 4". Just more weight, noise, and cost and less ground clearance.
If I forgot anything or made any mistakes I'm sure someone will let me know....