Actually, Porsche produced 47,928 Boxsters between the yrs. '98/'99 (22,063) and '99/'00 (25,865). Porsche list these as cars produced in those calendar years, but does not identify them as model yr. - There were '98 and '99 MY produced in the first number and '99 and '00 MY produced in the second number. Production increased each of the early years so I think your number of '99s produced is maybe 1,500 or so low.
Engine serial numbers have no correlation to chassis VIN numbers. Though they may be sequential (maybe), that doesn't mean that all the replacement engines were of a certain 'run'. For example, of a batch produced, X number may have gone toward production and Y number to replacement inventory. That would mean that the replacment engines would have a
hodge-podge of sequencing allowing no conclusion to be drawn. Nor is there any reason to assume the replacement engine were allocated FIFO (First In, First Out) - a 'late' serial numbered replacement engine may have been sent out while earlier numbered engines remained shelved - no way to say for certain. Also, certain #s may have been sent to PNA while others went to Asia for example... or may not have.
So far as engine replacement, there is no single factor here, but I believe the major one to be RMS failure, followed by engine porosity and liner failure (late '98 and early '99) while the rest are simply that portion of accepted mfg. defect.
Most informal surveys tend to support a 25-30% failure rate for RMS, and while that may 'agree' with your supposition, I think it's dangerous to draw any conclusion because Porsche is simply not saying, and likely never will.
I don't know how sound your logic is, but I for one don't think you're nuts.
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