Henry Huntington purchased a copy of the Gutenberg bible on vellum (of which only a dozen or so copies exist) in 1911 for the then record price of $50,000. At that same auction, a copy of Caxton's edition of Mallory's Morte d' Arthur sold for $42,800. But those were purchases by wealthy collectors intent on building world-class collections.
From my limited knowledge of such sales, rare book and manuscript prices could vary wildly based on many factors: provenance, relative scarcity of copies, condition, binding, whether sold by lot or en bloc, etc. Sometimes a real bargain could be found for only a few hundred dollars (if you were a shrewd and knowledgeable collector/buyer), but more often than not prices would be in the thousands. I don't think $3,500 for a copy of the Pnakotic Manuscripts is at all unreasonable.