The engines are physically the same. Later 3.0s had a larger plenum but this can be transplanted by replacing the two rubber intake ducts that feed the throttles, and a longer throttle cable, or the old plenum could be retained.
If it's an automatic gearbox, the 2.5 will have an AR25. Would be best to replace this with an AR35 from a 3.0.
Manual gearboxes were also different but the consensus is that the 2.5 gearbox will handle the 3.0 with no problem so not worth swapping it in this case.
Diff ratio would probably have been different. Again, depends on auto or manual. Could swap the diff for a 3.0 one or retain the 2.5 one and get better acceleration at lower speeds against a higher cruising RPM and perhaps slightly higher fuel consumption.
Engine management ECU firmware was the same as well, IIRC. Fuelling is based on the measurement from the MAF so the system will cope with the extra fuel demand. Fuel injector flow rates were the same.
Kevin