As Laurel said, it’s likely that <ruyflare> is an alternative spelling of the word rifler. And it seems to be unclear whether the word rifler is related to the word ruffler.
The OED traces ruffler back to the verb ruffle, which is says is of uncertain origin, although it does hint at the possibility of a connection with the note “With sense 6 compare rifle v.1” (the verb corresponding to rifler).
The verb rifle is supposed to be “< Anglo-Norman ryffler, rofler, rufler, rufeler” (OED); some of these variants that look like they could give rise to a form “ruffle,” and in fact the OED lists, among the attested English spelling variants that it classifies as forms of
rifle, v.1, the β forms “[Scottish] pre-17 rufle” and “[Scottish] pre-17 ruffell”, but it’s apparently unclear if this is the origin of the words ruffle/ruffler.
The spelling <ruyflare> is likely to indicate a vowel in the first syllable that is the same as the reflex (in some M.E. accent) of Old English /yː/. According to Notes on English Etymology by Walter William Skeat (1904):
The ui in build is a southern M. E. symbol for the M. E. sound arising from A. S. ȳ, due in this instance to a (temporary) lengthening of A. S. y before ld. Cf. bruise from A. S. -brȳsan (in tō-brȳsan); and buy from late A. S. bȳ, for A. S. byg- in
byg-eth, pr. s. of bycgan.
(this quote was found by Ricky for his answer to the following question: Why is "build" spelt with a "u"?)
The phonetic quality represented by this digraph seems a bit hard to determine; note that “build”, “bruise” and “buy” all have different vowels in modern English due to dialect mixing, and this source of variability existed already in Middle English. So perhaps the scribe wrote “ruyflare” but pronounced [riːflər], or perhaps [ruːflər]. I don't know if there is any way to make an educated guess about this; possibly an examination of the use of the digraph "uy/ui" in other parts of the manuscript would be fruitful.