2)  What can we learn from the mise-en-page (page layout) and how are these properties typically described?

How many columns per page? 
Single-column / double-column / triple or quadruple column (rare!).  Scribes planned their copying in advance, and their most basic choice was "how many columns per page?"  (Compare "mise-en-place" for chefs setting out the spices and other ingredients, pots and pans and instruments, etc. for a given dish, or a carpenter calculating how much and what kinds of wood, how many and what kinds of fasteners, and what kinds of machine or hand tools are needed to produce a given object.)

How many lines of text per column? 
Scribes methodically pricked and ruled their parchment or paper before writing according to their calculation of the lines of text in their exemplar MS vs. the size/quantity of parchment or paper substrate stock they had for the job. 

How was the page pricked and ruled?  Drypoint (only a groove--rare, early or late fine work).  Plumet (lead grey) late C11 and onward.  Ink, C14-15, except Humanist texts.  C15 Humanist scribes' MSS were often ruled in drypoint.  Also compare paleography for the Humanist shift from C12-15 Gothic "modern" script to imitation of the older Carolingian (C9-12) script in the Florentine litterae antiquae or "antique letters."

How tall and wide is your text block, from corner to corner?  
Measure from top to bottom corners first, in centimeters.  Then measure from side to side corners, in centimeters.  Always record the height first.

How are rubricated capitals distributed and decorated?
  Capitals are measured by the number of lines they take up (e.g., 2-line, 3-line, 6-line, etc.) and described by color and decorative embellishment (e.g., fine "penwork" extending into margins, "historiation" or faces/scenes set into the capital).  Can you detect "guide letters," small usually lower-case letters in the spaces left for the capitals to guide a later rubricator?  Lack of guide letters may indicate the scribe rubricated the MS while writing it, page by page.  (See example in my envelope of breviary leaves!)

Does the page have header titles, marginal notes, "manicles" (pointing hands), or other "apparatus" to guide readers?  Later MSS came with such aids in the original scribe's hand.  Later readers (in later scripts/hands!) often added them as they found need.  Sometimes, you can detect multiple "campaigns" or layers of annotation that have accumlated during the life of the MS.

Does the leaf have "page numbers" on one or both sides?  OK--trick question.  Medieval manuscript leaves were never numbered.  You did not have so many books that it required numerical assistance to find your way around them.  That's what the illuminations and rubrication were for.  If you see penciled numbers, they were placed there by modern manuscript dealers or museum curators.  Typically even modern curators only "foliate" MS leaves with a number only on the right side of an opening.  Page sides were distinguished by "r"  or "recto" for the right side of a leaf, and "v" or "verso" for the  back of the recto.  E.g., l. 235r is the right side of leaf 235, and its opposite is l. 235v.  Early printed books' pages also were not numbered.  In the late C15 to early C16, printers foliated them (e.g., "F.140" in the upper right corner of the recto), and only in the C16 did they begin paginating both sides of the leaves.

Do illuminations take up a full page, half-page, etc., and how are they composed?  (Also see iconographic analysis.)  Scribes had to pre-plan illuminations as carefully as the initials marking major sections, leaving space for their insertion by other artists.  Scribes rarely, almost never (?) illuminated the manuscripts they wrote.  Can you detect original ink/hand scribal instructions to the illuminator regarding the content designated for a given space (see capitals above)?  For more on illumination and rubrication strategies, see textual and iconographic analysis.

Does the text start above the top ruled line (before 1200) or below the top ruled line (after 1200)?
  In 1960, N.R. Ker published a four-page article that rocked the codicology world by arguing (successfully) that in about 1200 a revolution in scribal practice gradually overtook the Anglo-European world.  Obviously, starting below the top line wastes a space that could be used for text?  Why do it?  One clue--at about the same time, scribes increasingly came from non-clerical, non-monastic occupations, such as notaries, theology or law students trying to scrape up some cash, and eventually professional "clerks," later "scriveners," whose profession was copying for profit texts of all kinds.  It was a new "gig economy," and a hard way to make a living.  Dickens' Bob Cratchit from A Christmas Carol and Melville's eponymous tale of Bartleby the Scrivener mark the end of the scribes' common appearance in C19 business culture, though they persist in the business of making wedding invitations, etc. The secular scribes' predecessors, the clerical scribes, copied  mainly religious texts, for the good of their souls.  N. R. Ker, "From 'Above Top Line' to 'Below Top Line': A Change in Scribal Practice," Celtica (5 (1960) 13-16; rpt. Books, Collections an dLibraries: Studies in Medieval Heritage, ed. Andrew G. Watson.  London, 1985.  71-74.