Yes, the alternator and in most cases the battery need to be relocated.
It doesn't matter how you run the cable... If you're unsure get a 1JZ cable and build a bracket or get a universal and cut to fit.
The BOV just needs to go before the throttle body (the closer to the throttle body the better) and it's reference needs to come from a vacuum port AFTER the throttle body.
It's best to supply the waste gate's reference line from as close to the turbo as possible. If you're running a boost controller that will sit in the middle of the line.
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