your two series 1) x-qatal vayyiqtol and 2) vayyiqtol x-qatal are a good
distinction for discussion.
however, i would not put parentheses around the vav in (w)X-qatal:
wayyiqtol-->(w)X-qatal-->wayyiqtol
"no vav" would signal a structural break, either on a large scale like new
section, or a small scale like parenthetical insert.
as for pluperfecticity, one will not be able to get at that by paragraph
position. paragraph initial x-qatal can be either pluperfect (jona 1.5),
simultaneous or sequential (gen 4.1).
on the otherhand, paragraph position does help distinguish a
literary/dramatic use of x-qatal, that is, a marked, sequential use of
x-qatal, which otherwise marks a break up either of time flow or of
structure. (jud 6.21, ex 9.23, gen 19.23-25 [no vav!], est 7.6-8.1.)