First, a general reminder that you must pay close attention to Sidwell's notes. They will alert to you oddities that will otherwise cause your brains to hurt.
RLM 1.1(b) second paragraph: "quaestionibus" has to be taken as something like "troublesome points," "issues of dispute," "disputed points" ("things that provoke questions"; within its classical semantic range). The "de" at the start is, I think, more likely introducing the subject: "As for those ...." "Unusquisque" is nominative. "As for those issues that are read but not, by chance, understood, let each ...."
RLM 2.1(i).2 (line 2): "Qui septenarius sacratus numerus": "septenarius" means "containing seven", but here must simply equal "seven". "This sacred number of seven", "This sacred number, seven,..."
(lines 2-3) "si matutino ... tempore": make sure you read Sidwell carefully on this. What he means by "all depends on tempore" is that "primae" etc. are genitives governing "tempore": "at the time of prime".
(lines 9-10) "matutinis .... completorio": in contrast with the previous list, these are all ablatives of time.
2.1(ii).1 (line 1): "Iam ... digessimus": "We have already arranged..." (from "digero").
(line 3): "Deus in adiutorium": as you might deduce from the italics, these are titles of hymns or parts of the Mass.
(line 7): "Kyrie eleison" in modern spelling (from the Greek: "Kyrie" is a vocative meaning "Lord", and "eleison" an aorist imperative second person singular of the verb "have mercy," "pity"; Κύριε ἐλέησον). These are the first words of the Mass.
"missas": from the last words of the Mass, "ite, missa est."
RLM 2.3 (line 25): "Aequalis" is vocative.
(line 29): "Praesepe" is nom.
