Yes, the IP will give the same power output regardless of whether you have it on a 603 or 606. The injection quantity is the same, so the power output will be the same. Horsepower increase comes from additional fuel and timing. The difference between the 3.0 and 3.4 pumps is largely in the torque capsule and RPM limiting. The 3.0 pump will pull hard to ~4600 RPM before tapering off fuel while the 3.4L pump will fall on its face ~4K with the 3.0L engine. It's just how they're tuned for the different displacements.

The bottom end on the 60x engines is extremely durable. If there's no noise or symptoms of wear, leave well enough alone.

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Current stable:
1995 E320 149K (Nancy)
1983 500SL 120K (SLoL)

Black Sheep:
1985 524TD 167K (TotalDumpster™)

Gone but not forgotten:
1986 300SDL (RIP)
1991 350SD
1991 560SEL
1990 560SEL
1986 500SEL Euro (Rusted to nothing at 47K!)