If my bike was to be one with the performance kit, what effect would that have on its value?
It has the silentium race pipes, larger 40mm headers and been rejeted. It also has the gold rocker covers. As I purchased it 21 years ago with 9000km on the clock imported from Italy the chance of some one buying the bits and putting them on would be low I would think.

I don't think it would have any effect on the bike's value unfortunately. Ian Falloon mentions 100 more powerful red Pasos in his book but even if they really existed there's no documentation to prove this. As with some other special models Ducati built they just continued to use the same VIN number type so there's no way to differentiate between a standard Paso and one of the 100 (or a Limited).

A friend owns a modified 916S. Again Falloon mentions the S-version as a limited version that was built and positioned between the standard 916 and the SP. The VIN is the normal 916 one and there`s basically no existing documentation of an S-model existing at all so there's no way (other than trying to contact the Ducati factory) to prove it is one.
Meanwhile the guys who worked on the development of those Ducatis are retired and documentation in the factory seems patchy if existing at all.

Also, as mentioned in Ian Falloon's book: most of the performance kit parts became standard a little later on (e.g. the larger diameter headers).
This is typical for the Cagiva bikes, by the way.