When I bought my 00 it has a PCII and Moriwaki high pipes. Is it worth the cost to change from my PCII to a new PCIII?

I'd say that if it works fine, then no.
If and when it dies, then spring for a new unit.
Unless there are specific needs that only the PCIIIUSB can offer over your existing unit.

The one I'm looking at is the PCIIIR. It has the Ing modul built in.

The PCIIIr (which I have) has the capability of tweaking the ignition timing.
That was the main difference between prior units (PCII and PCIII).
While nice for race teams, it's overkill for the casual rider or one who doesn't have the resources to monitor the engine during testing.

The engines are at a high state of tune already, and it doesn't take much to cause a overheating, pre-ignition, or detonation state if advanced too much.
Be very careful if you decide to play with the timing.

The PCIIIUSB is modular in design and has various add-on modules for more functions.
Like ignition timing, quick-shifter, etc. They even have a hub for everything to plug into.
Another slight advantage it has over the older units is that it samples the engine every 250 RPM vs. 500 RPM of the older units. On paper it allows more fueling accuracy.

If you plan on trying to optimize your tune then yes get the 3usb if not then don't mess with it. The tuning capabilities of the 3 are far better then the 2. Usb is better an easier then serial. You can tune at 250rpm increments instead of 500. There is the accelerator pump feature among others. Also you can tune each cylinder and run the bike on two different maps.

And waldo just so you know the ignition feature on the 3r has no effect on our bikes. Its pretty much pointless. Thats why you can convert 3r maps to the usb format. I'm running a 3r map right now from thorsten with my 3usb. If there was any sort of ignition adjustments nobody would be running 3r maps on their usb's cause they could potentialy destroy their bikes. So if you haven't gotten that 3r yet good. Get the usb instead.