On the Student Resources page you found a list of "Dos and Don'ts" for transcribing Greek minuscules for the MOTB Greek Paul Project. As you looked through the lists, some of the items may have been unfamiliar. This page is here to help familiarize you with those items.
Where there is a parallel reference in the Transcription Editor Guidelines PDF document, it is noted below.
Note that it is just as important to record those things that you are supposed to record as it is to ignore those things that you aren't. The reconcilers who evaluate your transcription later will need to spend extra time adding or deleting things that you didn't record but were supposed to, or did record but weren't.
1) Inscriptions and subscriptions
Inscriptions and subscriptions are like expanded titles given at the beginning and ending of a letter. The inscription will most often be limited to a brief descriptive title (e.g., προς τιμοθεον Α) while the subscription often includes other elements such as author, location, or occasion of the letter.
Cf. Transcription Editory Guidelines §11.3 - Inscriptio and Subscriptio
Corrections are edits made to the original text as written by the original scribe. Corrections may be made by the original scribe (first hand) or by one or more later correctors. There are many ways corrections can appear in a manuscript: an erasure, overwritten text, text written between words, a strikethrough, dots over or under a word (to indicate deletion), etc.
Do your best to keep your eyes open for possible corrections and, if you find one, try to decipher as best you can what the original hand read and what the correction reads.
Cf. Transcription Editory Guidelines §4 - Corrections
3) Alternate readings
Alternate readings occur when either the original scribe or a later corrector knows about a variant reading of a portion of text and records it somewhere on the page of the manuscript. Typically, alternate readings are marked with a plus-shaped sign (+) or an asterisk (a plus sign with a dot in each quadrant).
Cf. Transcription Editory Guidelines §4.7 - Alternative Readings
4) Column and page breaks
Some manuscripts are written with more than one column of text on a given page. You will need to record where one column ends and the next begins (including any words that span the break). Page breaks are pretty much automatic, but you will need to be aware of and record two phenomena: (a) When a partial verse occurs on a page (initial or final portion of the verse); (b) When a word spans across a page.
Cf. Transcription Editory Guidelines §3 - Page Layout (Break)
5) Presence/Position of commentary text
In manuscripts where the biblical text is interwoven with commentary text, you will need to record the presence of commentary text (you do not need to transcribe it). On pages where the biblical text is in one large block surrounded by commentary text, you do not need to record the presence of commentary text.
Cf. Transcription Editory Guidelines §8.1 - Commentary Manuscripts
6) Nomina sacra
Nomina sacra (or sacred names) are particular abbreviations of certain words (mostly proper names) in the biblical text. They will need to be recorded as such, with the overline noted if present. If those words that are often thus abbreviated appear in their full, unabbreviated form (e.g., ιησους instead of ις) you will need to transcribe the full form (as it appears) though not mark it as a nomen sacrum.
Cf. Transcription Editory Guidelines §7.1.1 - Nomina Sacra
1) Moveable nus if absent
In certain forms of verbs and nouns, the final nu is optional (moveable). It is typically present or absent depending on whether the first letter of the next word begins with a vowel (moveable nu is present) or a consonant (nu is absent). This helps to "smooth out" the vocalization of the text. This is very common in words like εστιν or γεγονεν.
The bottom line here is: Record what you see. If the final nu is present, record it; If it is absent, don't record it.
2) Iota subscripts and adscripts
In the dative singular, the iota is typically subscripted (e.g. τῳ), but sometimes it will appear in a manuscript as an adscript (τωι). In either case, whether subscripted or adscripted, you are not to record the iota.
Cf. Transcription Editory Guidelines §7.2.1 - Transcriptions of Minuscule Manuscripts
Ekthesis occurs when the scribe writes a larger and sometimes ornamented form of a letter that extends into the page margin. This typically happens at the beginning of a new unit. Record these letters as normal letters, as if there is nothing unique about them.
Do not record any punctuation.
Cf. Transcription Editory Guidelines §10 - Punctuation
5) Capital letters
All letters of the biblical text should be transcribed using lowercase characters, even those that appear as capitals in the manuscript.
Cf. Transcription Editory Guidelines §6.1.3 - Capitals
Rubrication is when some of the letters of a manuscript are colored red (typically). In most manuscript images, you wouldn't be able to tell the difference anyway, but don't record rubrication.
Cf. Transcription Editory Guidelines §6.1.1 - Rubrication
7) Lectionary notations
There are a variety of lection notes scattered throughout many of the manuscripts you'll transcribe. The most common are the shortened forms of τελος (end) and αρχη (beginning) that typically occur as a pair in between sentences. Do not record any lection notes.
Cf. Transcription Editory Guidelines §8.2 - Lectionary Notations
8) Line numbers
You do not need to concern yourself with the line numbers in your transcriptions.
Cf. Transcription Editory Guidelines §3.3 - Lines
Often times, prior to the biblical text you will find a hypothesis (summary) at the beginning of a biblical book. You may run across this in your transcriptions (though it is unlikely, as the pages you'll transcribe are indexed to begin after they hypotheses). Sometimes these can appear to begin with an inscription, but it's really the beginning of the hypothesis (e.g., υποθεσις προς τιμοθεον Α). Do not record the title or content of the hypothesis.