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A 'clerical individual' (religiosae personae) surely means a member of a religious order. It would seem a curt description unless secrecy is involved. Elsewhere in the letter Barschius is conventionally reverential but lacks the piety of Marci and Kinner. We do not discover the messenger's identity (if it had been Moretus, Barschius would have said so), only that he or she was drafted as a witness to the transcription of the manuscript.
Oedipus Aegyptiacus 'the Egyptian Oedipus' of course means Kircher and Sphinx means any riddle: it was then schoolboy knowledge that only Oedipus could solve the Riddle of the Sphinx. Kircher went on to write a book called Oedipus Aegyptiacus but it was only published in 1652-4 and at this time he was famous as the author of Prodromus Copticus (1636). In the preface to that book he expressed his hopes that Coptic would prove to be the 'Oedipus' of hieroglyphics.
Barschius wants Kircher to 'correlate those characters of unknown devising with known letters' (characteres illos fictionis ignotae, literis notis manifestare). This is a free translation: a more literal one would run 'manifest in known letters those characters of unknown making'. The point is that Barschius assumes that the key to the problem is simply to identify the script.
He describes the manuscript he owns as containing 'pictures of herbs, of which there are a great many in the codex, and of varied images, stars and other things bearing the appearance of chemical symbolism'. Some have questioned whether he is talking about Beinecke MS 408: the description would apply to plenty of old books, and why doesn't he mention the naked women? But his aim is to persuade Kircher of the high seriousness of the puzzle, and a priest would probably refuse to look at any book which might be suspected of being pornographic.
It is of interest that seventeenth century herbalists could not identify the plants.
Barschius speculates, purely on the basis of the illustrations, that the manuscript concerns medicine and was written in Egyptian by a vir bonus, a 'good man'. He wants it translated for the benefit of boni, 'good men'. What exactly is a good man? One of ability and integrity no doubt, but also one who disdains the practice of medicine and conceals important knowledge causa plebeiorum occultandorum, 'to keep the common people ignorant'. The phrase has connotations of social class and I have translated it as 'a man of quality'
'Medical wisdom': Daniele Metilli points out that the transcription should be medicae sapientiae, not the non-existent word predicae which has previously been suggested.