There are extensive modifications available from respectable tuners like Manthey, RS-Tuning & some others. The modifications include expensive materials therefore it is more expensive to do than upgrade the ECU on a turbocharged engine.
Those companines, amongst some others, are also involved in Porsche racing activities, e.g. preparing the engines for Cup racers. So they know what they are talking about.
The normal GT3 MK1 have 350-354 PS at the flywheel. I have PSI 3.8 litre motor with 450 PS First I put the Cargraphic exhoust system (complete) with RS ECU and than it have 364 PS. After that I do the engine conversion to 3.8 litre with Cargraphic exhoust and it have 410 PS (lost about 20 PS with that exhoust), after that I put the heads from GT3 MK2 and PSI exhoust and than dyno showed 450 PS.
Not only the Mk1 GT3s were lacking horsepower, the first 996 Carreras did just the same. Porsche seemed to have some difficulties to put out engines with adequate numbers in high volumes.