for stage 1, i would get it all fitted up, all piping made, them remove it all and put stock parts back on so then it will be ready to go when you need it. i say this because stock N/A ecu's that use map sensors tend to have a metal if you turbo them. if you had the older 80 series 1fz you would have got away with it as they use the infamous flap style air flow meter.
once you have all the parts you could easily have it done and running again within a weekend.
when you get to stage 2 then put your already fabbed turbo setup and piping on at the same time as the new ecu.
also with the manifold, as awesome as the 6boost's are (i have one on my 1jz) i would go the cast manifold. its a 4wd and is going to see some harsh conditions (one would hope) and i honestly thing the cast manifold would tolerate more abuse.
just my 2 cents, good luck with your project!
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