The clue to this question is in the text itself. By using the word "respectively", Joyce is telling the reader to take the marks in the order he has listed them. For example the Collins Dictionary definition:
Respectively means in the same order as the items that you have just mentioned.
Since each description of the mark extends in length and extremity of instruction (i.e. "o do please stop" is much more desperate than "stop"), they can be associated with the extending length of each pause in punctuation. That is: the comma, the semi-colon, the colon and the full stop.
This rule governing the meaning of these four grammatical marks was set down in a book known as The King's English by H. W. and F. G. Fowler. It is interesting to note that Joyce appears to have referred to these scholars when constructing Chapter 16 of Ulysses. He repeatedly re-uses phrases and obscure words from that book in his chapter often, it appears, in mockery of its formal strictures. For example, he uses the construction "funny, very" which The King's English decries as childish, and repeatedly makes incorrect use of the word "individual" to refer to a person, which the King's English states is the mark of writers "without the literary sense".
It is worth noting that the punctuation marks in question are also used as diacritic marks i.e. dots and dashes above letters to influence their pronunciation. Such marks are used extensively in the passage which follows the list of "paper wounds".
that they ad bîn "provoked" ay ^ fork, of à grave Brofèsor; àth é's Brèak
— fast — table; ; acùtely profèššionally piquèd, to = introdùce a
notion of time [ùpon à plane (?) sù ' ' fàç'e'] by pùnct! ingh oles
Of course this passage has been extensively "wounded", as Joyce describes it, by punctuation and diacritical marks. As has the intervening passage:
the circumflexuous wall of a singleminded men's asylum, accentuated by bi tso fb rok engl a ssan dspl itch ina
The beginning of which can be read phonetically as "bits of broken English". The image conjured by the literal reconstruction, a wall topped with "bits of broken glass and split china" looks rather like a sentence full of diacritical marks, as does the jagged rendering that Joyce has given in.
Furthermore, there are a number of wordplays in this sentence as is typical for Finnegan's Wake, in this case, to do with punctuation. The wall is "circumflexuous" which sounds like "circumfluous", i.e. to surround something. But the spelling is redolent of "circumflex" which is the diacritic mark ^. It is "accentuated" by the bits of crockery, which means "make more noticeable or prominent", but diacritical marks are sometimes known as "accents".
Finnegan's Wake makes many allusions to languages other than English, in which such marks are common. Indeed in referring to the letter as a " Tiberiast duplex", Joyce is invoking Hebrew. The canonical pronunciation of various Hebrew holy texts, often using diacritics, was established in the city of Tiberias between the 8th and 10th centuries.
Gibson, Andrew. "Joyce through the Fowlers: ‘Eumaeus’, ‘The King's English and Modern English Usage.’" European Joyce Studies, vol. 22, 2013, pp. 225–244.
Mecsnóber, Tekla. "A Notion of Joyce’s Time: Interpreting the Diacritics of Finnegans Wake" Genetic Joyce Studies, issue 14, 2014