3)  What can we learn from MS paleography (ancient writing) and how are manuscript scripts (writing styles) and hands (individual scribes' habits) typically described?

What is the script of the main text?  Scripts you are likely to encounter will be forms of Gothic writing, fairly complex letter forms that differ from one era to the next.  That means the script can help you approximately date even a single loose leaf from a broken manuscript.  The oldest script you are likely to encounter, very rarely, will be Carolingian, possibly originated by Alcuin (724-804 CE), Charlemagne's English master in the C8 and in use until about 1100 CE.  It is a rounded, relatively simple, seemingly "modern" script that most American students find easy to read.  Proto- or Early-Gothic scripts after 1100 complicate the letter forms, and Gothic Textualis or Textura (ca. 1350-1400) and Gothic Littera Bastarda (ca. 1400-1500) grow even more convoluted and tightly knit together (i.e., "textura," letters in words that look like woven fabric). 
     To detect a script's passage on the road from Proto- to late forms of Gothic, look for instances of "biting," the intrusion of one letter form on the next, as when an "o" or "c" or "e" touches an adjacent letter.  When sequences of vertical strokes (minims) used to create the letters "i," "l," "n," and "m" begin to bite at top and bottom, the result can be a nearly impenetrable thicket of seeminglly identical strokes.  At such times, if you are a habitual Gothic script reader, your mind gestalts the line differently from the modern reader and you see no problem.  The rest of us stare in amazement.  The small letter "t" begins its Gothic life as a Greek "tau" with no ascender above the horizontal stroke.  By Textura/Textualis, the ascender has risen above the crossbar.  Other tell-tale changes can be learned if you have the patience and time to practice.
     Think of paleography as a long-term project, nothing to be learned in a semester or even a year.  Be patient with your mind/brain and give it as much practice as you can.
       For more detailed descriptions of typical differences, click here, but note the page's links to Diana Tillotson's wonderful Web tutorial mostly have been lost as of December 2020 when Adobe ceased supporting Flash.  For the best currently paleographic tutorial in Latin scribal practices, see the HMML School's Latin site.

What is the script of header or marginal "apparatus"?  Remember that medieval manuscripts are in use for hundreds of years, and during those long passage of time, scripts change.  Readers effectly "date" themselves as they annotate, and the relative density and content of their annotations can help you determine what kinds of readers used the MS, and why.  (Also see textual and iconographic analysis.)

How might the script of your MS correspond to its content, as well as its era of production?  In later eras, earlier scripts acquired their own "content significance" by  association with certain kinds of common books in which they were found.  By the C14, most traces of Carolingian script had been lost to damage or to recopying in the "new" Gothic scripts.  Because all genres of books (theological and secular) were being copied in the same hand, nothing special was attributed to its use and users apparently found it easy to read, especially when "reading" was effectively just looking for cues for recitation of memorized prayers and other sacred texts.  More careful parsing of unfamiliar texts put greater strain on readers, and Gothic letter forms became a barrier to that kind of "deep reading."  C14-15 Humanists, in particular, grew to hate Gothic scripts because they sought out long-lost Greek and Latin classics in MSS preserved only in rare Carolingian-era scripts (starting especially with Petrarch [1304-1374]).  In the early 1400s, Florentine scholars Poggio Bracciolini (1380-1459) and Niccolò de' Niccoli (1364-1467) deliberately created a script imitating the Carolingian script, Niccoli adding a cursive (connected) form that could be written more quickly while still remaining highly legible.  After Humanist writing became common, Gothic scripts were used to indicate "ancientness" or "sacredness," and that tradition carried over into type font design for moveable type  printing.  Chaucer's earliest Renaissance print editions were produce in a Gothic (also "black letter") font.  See, for instance, the front page title of The New York Times or The Washington Post!  This also connects to the textual and iconographic analysis of the MS.