Recognizing the shift of the Covenants from the Old Sinaitic one to the New one, the Messianic Judaism maintains fundamental significance of the Torah, especially with regard to those statutes, which are called eternal by G-d. Such attitude towards Torah discards any attempt to explain the word “eternal” sort of emphatic meaning in Hebrew. All statutes are in force “till all be fulfilled” (Matthew 5,18) with the single pecualiarity that part of these statutes are executed by Y-shua‘ Himself (e.g. those requiring the Temple for the perfrormance of sacrifices, Y-shua‘ Himself being the Temple, but His Sacrifice replacing and superseding all Temple sacrifices). The Torah and the Gospel do not contradict one another, however the New Testament testifies fulfilment of the Old Testament: nothing is crossed out and nothing drops out! It seems therefore reasonable to rearrange the traditional order of the books of the NT to conform it to the order of books of the OT:
The Gospel and Acts match and continue Torah,
The Book of Revelation matches and continues the Prophets,
The Scriptures are continued mainly with Epistles to Hebrews (to all Jews) and James (to Messianic Jews in diaspora). 
For the Messianic Judaism are essential the 11th chapter of the Epistle to the Romans, and the epistle to Messianic Jews and Messianic gentiles Galatians. The latter can be comprehended in a controversial polemic sense of an extremist negation of the justification by works (in contrast to James 2, 24-26), not only by faith. Therefore the words of 2 Peter 3, 16 can be applied to it. 
To Messianic Jews and gentiles the episteles of Peter, John and Jude are addressed. 
Messages addressed to Messianic gentiles (as to Romans, Corinthians) can hardly be considered a continuation of the Hebrew Bible at all.
As for the famous statement of 2 Timothy 3:16, it refers to the time before the formation of the New Testament canon. Therefore it has in mind the Hebrew Bible and the Gospel only, while the latter had not been canonized yet in modern 4 versions (which did not exist then at all).
All epistles are practical teachings (Midrashim) that are not necessary to include in annual reading of Scriptures for the Jews, except Hebrews and James. The first represents a short messianic exegese of Scriptures whitnessing Y-shua‘. The latter represents Hellenistic Jewish preaching of G-d's and Torah wisdom in the light of the Gospel.  (Cf. here a proposed sequential reading of the NT in the order of Parashot).