Glad I can help. I am not really deep into the material, but not entirely unfamiliar either. And I have a thing for old books / scriptures in general as documents of their times. So it's not like there's nothing in it for me!

To clarify, there is nothing except the preface written by the government. It is only transscripts of found documents, with the only metadata added being the identification of certain authors via handwriting or other information. According to the preface, the documents have been published as a warning for bavarian citizens about joining an organization, or as is written 'sect' like this. At this time , Secret societies have also been recently forbidden and therefore been persecuted - which more than likely led to the collection of these documents.

A bit back to the OP: A good, open tool for reading in these 'Fraktur' typesets may be 'tesseract ocr' with a specialiced dataset, I think I used it for a book years ago. It's a bit fiddly to use (command line only) However, the difficulty would still lie in automated translation. The German back then - especially in written form - can be vastly different to the contemporary.

To your questions:

I) Yes, it's a really simple cypher, letters are replaced by one corresponding number each - you find according sequences of numbers throughout the book.

II) It says the used calendar is yezdegerdian, or persian, and lists the months names.

III) Yes, exactly

V) Talked about creating - what use it would have, how it should be organized etc. really briefly. They appear to be in negative terms with the jesuits. It is mentioned that the jesuits failed to overtake or abolish a certain committee which seems to please the author. Unfortunately a large chunk of this passage seems to be lost. The 'progress' in these parts seems to mainly mean installing members in good positions.

XI) No ritual guide, more like guidelines on how to handle new / prospect candidates for their 'leaders'.

XXIV) Turns out I misinterpreted something upon skimming - 'Quartblatt' doesn't refer to a quarterly magazine as I initially assumed, it's just a certain format of paper sheet. Old german is tricky. It is noted that instructions were given to a person leaving for a longer period of travel.

XXXI) There are a lot of number codes in these letters, hard to make connections without a full transscription. It seems they write about 'replacing' someone. Some member is thought to be a jesuit. Talk about a creating a secret circle of chosen persons, about 'using' someone.

XXXIII) Yes I referred to the cypher, it is really used a lot in these letters

XXXV) Some of the info might maybe useful in a certain context. One noteworthy entry describes again an inner circle, or 'other System'/'expanded System'. Any regular member of the order should under no circumstance know about it, and instead advance in the 'normal' order degrees. Members of the 'other System' have a certain key sentence, so they can identify each other.

XXXVII) The beginning talks about a possible chapter being founded. Interestingly enough after going through the journal, there again is talk about 'our System' in the second part

XLI) I might be mistaken again, it says a Freemasonic 'table', with the annotation it is found at the end of the book. As far as I can tell, it is not there though. Maybe it refers to the cyphers / codenames in the beginning

XLVI-XLVII) Again the 'System' is mentioned, also mentions Rosicrucians (not in good terms with them either). They talk about the persecution of secret societies in Bavaria. 'Rome' is mentioned which is a bit confusing at this point, because while it is the code for Vienna, no other codes seem to be used in the letters, maybe it's literally rome. Again probably needs a full transscription/translation.