That is - the word העלמה can be found three times throughout T'nach. This is a sentence created by stringing together words from all three Pesukim. Roughly translated as - The girl "went out" (Targum translates זונה as נפקת ברא) was called "Mother" (reference to the Virgin Mary) and gave birth to a son.
This is a rather ingenious bit of polemic on the part of the Tiberian Masoretes (and one of the few bits of biographical information that we have on them). Living in 7th century Roman Palestine they must have heard the הנה העלמה הרה speech in the course of their "Seder Hayom" -(referring to the debates the Christians would raise on this subject?) and they took this opportunity to voice their own opinions on the "immaculate conception". Source: Igrot Shir.
2. Sefer Ha-Tishby - s.v. יתוש
In the notes of R' Yeshaya Pick Berlin  we have the following comment:
אם תזוח דעתו עליו אומרים יתוש קדמך (סנהדרין לח
to which the copyist adds:
והבן זאת שבא לתרץ כמו שהק' בשרש זקק וחרף
as is explained in the notes there. The entry for Yitush precedes the entry for Yeshu even though alphabetically Yeshu comes first. The "hint" is obvious.
This is interesting in light of Bachur's supposed conversion to Christianity - here, and his close friendship with a Cardinal - here (that comment was removed in many editions as noted in the Mazuz edition).
3. Daat has a good many original polemical documemts online - here. My personal favourite is the אל תהי כאבותיך. This is what Graetz has to say about it (History of the Jews V. 4, Ch. VI):
In the entire history of Judeo-Christian controversy no such stinging satire had been produced on the Jewish side as that now issued by the physician, astronomer, historical student, and grammarian Profiat Duran. During the bloody persecution of 1391 in Catalonia, Profiat Duran, otherwise Isaac ben Moses, or, as he called himself in his works, Efodi (Ephodaeus), had been forced to simulate conversion to Christianity. He was joined by his friend David Bonet Buen Giorno. Both resolved at a convenient opportunity to abandon their hated mask and emigrate to Palestine, where they could freely acknowledge Judaism. Their affairs being arranged, Profiat Duran traveled to a seaport town in the south of France, and there awaited his friend. The latter, in the meantime, was sought out by or came across the Jew-hating apostate, Solomon Paul de Santa Maria, and was prevailed upon to remain a Christian.
What was Profiat Duran's astonishment when he received a letter announcing, with much exultant vaporing, the definite acknowledgment of Christianity by En Bonet, who exhorted him also to remain in the pale of his adopted faith. The letter contained an enthusiastic panegyric of Paul de Santa Maria, who had been taken into the favor of the king of Castile. Profiat Duran could not remain silent.
In reply, he inflicted punishment on his friend, and more particularly on the proselytizing Paul, in an epistle characterized by the keenest irony, which has not yet lost its sting. It pretends to assent to everything advanced by Bonet, and to confirm him in his resolve to remain a Christian, " Be not ye like your fathers" (Altehi ka-Abothecha) is the refrain throughout, and so artfully is this admonition employed that Christians used it (under the title Alteca Boteca) as an apology for Christianity. Whilst thus pretending to criticise the errors of the older faith, Profiat Duran dwells on the Christian dogmas, naively describing them in their most reprehensible form. He concentrates on the weaknesses of Christianity the full light of reason, Scriptural teaching and philosophic deduction, apparently with no desire to change his friend's intention.
A portion of the satire is directed against the Jew-hater Paul de Santa Maria, upon whom Bonet had bestowed unstinted praise. "Thou art of opinion that he may succeed in becoming pope, but thou dost not inform me whether he will go to Rome, or remain at Avignon " — a cutting reference to the papal schism distracting the church. " Thou extollest him for havingr made efforts to free Jewish women and children from the obligation of wearing the Jew badge. Take the glad tidings to the women and children. For myself, I have been told that he preached mischief against the Jews, and that the cardinal of Pampeluna was compelled to order him to be silent. Thou art of opinion that he, thy teacher, will soon receive the miter or a cardinal's hat. Rejoice, for then thou also must acquire honors, and wilt become a priest or a Levite."
Towards the end Profiat Duran changes irony into a tone of seriousness : he prays his former friend not to bear as a Christian the name of his respected father who, had he been alive, would sooner have had no son than one faithless to his religion. As it is, his soul in Paradise will bewail the faithlessness of his son. This satirical epistle was circulated as a pamphlet. Its author sent copies not only to his former friend, but also to the physician of the king of Castile, the chief rabbi, Don Meir Alguades. So telling was the effect produced, that the clergy, as soon as they dis- covered its satirical character, made it the subject of judicial inquiry, and committed it to the flames.
 The notes were recently discovered and published in the edition of מכון הרב מצליח. The edition contatins the notes of R' Meir Mazuz as well as loads of other stuff (the letters of the Pri Megadim, Shlomo Buiber's Toledot R' Elyah Bachur,etc. Ironically, the Bedatz wouldn't give a Haskamah on the edition containing the notes R' Shlomo Shick refuting Tishby's position on the date of the nekkudot becausd (from here):
יצויין שבראש הספר כתבו שקיבלו הסכמה מהבד"צ של העדה החרדית, "אלא שמאחר וביקשו מאתנו שלא להדפיס הסכמתם הנזכרת עם "קונטרס תורה שלימה" הנדפס כאן בסוף הספר (עמוד רצה), מחמת שמחבר הספר "תורה שלימה" התנגד מעט לדרכי הרבנים החרדים באירופה לפני כמאה שנה (עיין בסוף הספר עמוד שח בהערה), לכן לא הדפסנו כאן את הסכמתם כדמותה בצלמה. ומ"מ הם עצמם אמרו לנו שקונטרס זה חשוב ויפה מאד, וכדאי להדפיסו בקונטרס נפרד, אלא שכך דרכם שלא לתת הסכמות לספרים שהובא בהם דברי חכמים שלא לרוחם".
(i.e. he belongesd to the status-quo (non-secessionist) Orthodox) indirectly supporting Ha-Bachur's position.
An interesting source on the dating of the nekkudot issue is in the (I think Dan missed this in his article in Hakirah) is the Kuntres Pekuot HaSadeh no. 4 printed in the back of V. 9 of Sdei Chemed. ואכ"מ
[I am looking for a Kovetz Beis Halevi V. 3 which should contain R' Pick's hagahot to Mitpachat Sefroim, also a Kovetz Tiferes Mordechai V. 3 which contain the Yaavetz's hagahot to Me'or Einayim. If anyone's got them please leave a comment.]