GT-40 sputters at idle and acceleration

[RTSN]

Have 650 hours on a '99 Sport Nautique with GT-40. Ran out of gas to bone dry a few weeks ago. Started to experience rough idle and acceleration all the time.
Changed fuel filter, plugs & wires, cap & rotor. Checked fuel pressure and had ~ 35psi at idle; 38 @ speed. Nameplate says 39 psi, +/- 3 psi. Changed low pressure fuel pump.
Running perfect when cold now, but same stutter at idle and acceleration after a few runs.
Any advice?
Thanks!

[DanielC]

After 650 hours, and 13 years, it would not hurt to replace the spark plugs, spark plug wires, distributor cap and the rotor.
Those fuel pressures are normal. You may have not needed to replace the low pressure pump.