To be honest you don't need to be concerned about that. Much more important is getting the engine sat at the correct angle and height in the engine bay.
With the gearbox attached if isn't directly in line with the diff, it will smash the prop up, due to too much angle of the UJ's.
I'd get the engine setup first as far back as possible and ensure its sat at the correct height and angle before thinking about the exhaust.
Don't you have FJ20 engine mounts, or front cross member?
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