The SAIS is easy to delete with a Hewitt kit. 30 extra horsepower is 30 extra horsepower, chances are you won't regret getting a 2005+

. You're also getting a slightly newer rig, which does matter considering things like electrical connectors, rubber components, and interior plastics start to get brittle at age. The TB issue is over ratted, the VVTI motors are only interference when the VVTI is activated. I suppose if you break a timing belt at a full-throttle run with VVTI engaged you can bend all 32 valves, but that would only happen if someone was negligent in never changing the timing belt.
The VVTI rigs have the same exhaust manifold issues as the pre-VVTI motors and headers are slightly more expensive. Even with headers on a pre-VVTI motor, you might get a bit closer to a stock VVTI engine in power, but a VVTI motor with headers will still be 30 HP ahead

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My VVTI motor runs very, very well with LT headers, an exhaust, cold air intake, and tune. Great passing power with the midrange torque from the mods plus the VVTI upper-end horsepower.