Marty,
Sorry to hear you are having trouble, the teen years are approaching and can be a difficult and trying time with your 2.5L and more maintenance than normal is probably expected. I have a few questions for you and your little friend:
1. Is the 5500 RPM ceiling the same with load Vs no-load, i.e. with clutch in / neutral revving Vs in 3rd gear WAO? If the two situations have different symptoms please list the deltas in detail.
2. Are you handy with a multimeter, if so please test the MAF output voltage at idle and revving. This can be done on a 99 easily because it has a mechanical throttle you can physically grab in the engine bay and rev, while looking at the meter on the MAF. I have seen MAFs fail where the output voltage is >5v. You should see a voltage between 0-5v on the signal line. If you need the wire color, let me know. MAFs fail in other ways than over voltage, so swapping out for a known good MAF from a friends Boxster or the like is the easiest test. A good OBDII reader will tell you the reading while you are driving, might be easier.
3. Have you rebooted your ECU? You can either remove the battery Positive for 5min (make sure you have your radio code), OR remove the ECU itself (4x 10mm) for 5min, then reinstall. Its easy as 123 to remove and reinstall, its in the trunk behind the carpet on the drivers (USA) side.
4. This could be fuel pressure related, but I need the answer to #1 before speculating much further. The fuel pump relay is cheap and they do fail. If you free rev OK (Question1), then check the fuel pressure under load. If it drops then replace the fuel pump relay first, then change the fuel filter second, then the fuel pressure regulator, lastly the fuel pump. As separate steps; change, test, change, test, etc.
5. Below 5500 RPM does it feel "normal"? If not whats different?
Suggestions:
S1. I have seen a batch of bad gas, bad = lots of water, cause a somewhat similar issue. So just as preventative maintenance, get some water remover from the auto parts store. It is cheap and wont hurt anything. Use a double dose.
S2. Check your intake for leaks. If you have a post MAF leak, this could fit your symptom. Lots of ways to look for leaks, start with a physical inspection, rev up the engine while your heads in the engine bay, listen for suction sounds, then you could move to more advanced methods like spraying propane over the intake pipes, intake manifold, etc looking for the idle to pickup. Do this OUTDOORS. Please dont blow yourself up.
S3. Check your air filter to make sure a colony of rats is not using it as Hotel Porsche, or other obstructions. Look for something big and obvious.
Most Likely:
The most likely issue is either an intake leak, MAF failure, or Fuel Pressure drop.