Joining the bandwagon
I normally agree with you Lewis, about the massive waste of cash that is defence procurements. Though, as your quote from Pepys attests, 'twas ever thus...
I think your inflation and fleet size calculation was utterly ridiculous though. When Victory was built, Britain had an empire, in which slavery was still legal (and rather profitable too). These kind of warships also tended to last a bloody long time, it was quite possible for a ship to be in active service for a century (with the odd refit and period of being laid up). Crewing them wasn't all that expensive either, especially when you could dock their (terrible) pay to cover food, uniforms and the like.
Back then, if you earned £1,000 a year, you were able to employ large numbers of servants and live the life of the idle rich. Obviously one didn't earn ones money, that was far too common. One had land, or maybe investments...
Comparisons are tricky things, it was a different world. For example, the going rate for 100,000 troops to fight Napoleon was only £1m per year. That was the British subsidy to anyone who'd fight the French. We even (sort of) borrowed Portugal for £7m a year. The Royal Family buggered off to Brasil, we put a British officer in charge of the army, and sort of used it as a giant depot.
If you call it £1,000 = £1m in today's money, then you're probably not too far from the mark. In which case I reckon we could build HMS Victory now for well under £50 million. Even at BAe prices... If you were trolling, then I think you failed, due to re-use of your favourite hobby-horse.
Didn't someone find a flat-pack first-rater at Chatham a few years ago? All the pieces are numbered, so we could always put that one back together. Should be more useful than one of the Type 45 Destroyers at the moment. As someone above has said, it would also be very funny to surprise the Somali pirates.