plain and simple the stock ECU has more then enough correction to compensate for the extra displacement
the only mod needing to be done to the engine is the cutting of the block for the rear motor mount that is discussed in debt on John Monins web site
as far as the down pipe you will need to modify it some to fit with the extra width of the 3.5
by FAR the best damn mod that can be done to an NA 3000GT
