Yes our present constitution is the one that was drafted and enacted in 1973 but it is not exactly like the 1973 constitution.
As you pointed out, over the period of time military dictators namely zia and musharaf held it in abeyance and changed it at their sweet will with mere presidential orders and PCOs later validated by 8th and 17th amendments.
Although 18th amendment went a long way in purging the constitution of these impurities, yet the present constitution is not exactly like the original 1973 constitution. 18th amendment did not revert completely back to 1973. Thus, while some changes made by zia and musharraf have been done away with, many articles and clauses still remain intact in the constitution as amended and inserted by the two military regimes.
Some examples would suffice:
-Zia changed the nomenclature and introduced the word majlis-e-shoora in place of parliament. 18th amendment doesnt touch that.
-zia made objective resolution a substantive part of the constitution by inserting article 2A----This remains unchanged
-Musharraf increased number of seats in national assembly and senate and kept permanent and increased number of reserved seats in parliament for women.----This change remains intact too.(and rightly so)
Similarly 18th amendment did not touch article 239. Thus Article 239 in the constitution today is the one that was introduced by Section 3 of the Constitution (Second Amendment) Order, 1985, P.O. No. 20 of 1985 (w.e.f. March 17, 1985)
and it(article 239) says and u have quoted above:

Article: 239 Constitution amendment Bill

[239. Constitution amendment Bill.-(1) A Bill to amend the Constitution may originate in either House and, when the Bill has been passed by the votes of not less than two-thirds of the total membership of the House, it shall be transmitted to the other House.

(2) If the Bill is passed without amendment by the votes of not less than two-thirds of the total membership of the House to which it is transmitted under clause (1), it shall, subject to the provisions of clause (4), be presented to the President for assent.
(3) If the Bill is passed with amendment by the votes of not less than two-thirds of the total membership of the House to which it is transmitted under clause (1), it shall be reconsidered by the House in which it had or originated, and if the Bill as amended by the former House is passed by the latter by the votes of not less than two-thirds of its total membership it shall, subject to the provisions of clause (4), be presented to the President for assent.
(4) A Bill to amend the Constitution which would have the effect of altering the limits of a Province shall not be presented to the President for assent unless it has been passed by the Provincial Assembly of that Province by the votes of not less than two-thirds of its total membership.
(5) No amendment of the Constitution shall be called in question in any Court on any ground whatsoever.
(6) For the removal of doubt, it is hereby declared that there is no limitation whatever on the power of the Majlis-e-Shoora (Parliament) to amend any of the provisions of the Constitution.]

so where in the above mentioned article(239) is the case of disagreement between the two houses and where is the rejection of the bill discussed??

The provision of 90 days, where is it???

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Why not !?