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Noticed Druumbowe made three edits to the "descendants" sections which seperates Sultan Ali of Johor from the "house of Bendahara". He made the following points, from my observations of his edits:
Sultan Mahmud Muzaffar Shah was the Sultan of the Johor-Riau empire. Based on sources in google books as well as a few books which I personally have from the google book collection, Muzaffar Shah was the de jure head of the original empire, for by the Dutch and British who intervened in the Singapore founding had broken it up into two. See . A History of Johore, by R.O Winstedt, provides a genealogical tree in pg 185 showing Muzaffar Shah as the "Sultan of Lingga". By practice he has authority over Lingga and not over the other parts of the original empire. 
Seperated Sultan Ali of Johor from the section of "House of Bendahara (Johor)]]. While Sultan Muzaffar was also descendewd from the Bendahara Sultans of Johor-Riau , it was Sultan Hussein who obtained the Johor regalia and hence the legitimacy as the head of the House of Bendahara (Johor). I admit that there was contention between Hussein (later his son Ali) with Muzaffar, as stated in . But again, it was with Sultan Hussein, rather than Muzaffar whom he ruled Johor. By then it was Temenggong Abul Rahman and not the Sultan who had power over Johor-Singapore , but the Temenggong swore allegiance to Hussein and not Muzaffar. 
As for Sultan Ali of Johor, while Temenggong Ibrahim increasingly took power from the Sultan, but between Sultan Ali and Sultan Muzaffar it was Ali who seen as the legitimate ruler of Johor. As far as I see from the sources, Sultan Muzaffar, was not the head of the House of bendahara (Johor). Also, your edit to claim that "Sultan Ali" as the pretender was not substantiated. I did a book search, and sources explicitely saying that he had no powers was not proven. He did have a little power, and it was with the British which Sultan Ali and not Muzaffar issues dealings with. []
By matter of info, I would sincerely urge that you may be willing to discuss contentious issues so as to resolve any misunderstandings as a matter Wikipedia:Assume good faith through discussion talks, so that we can create an article based on accountable facts Wikipedia:Citing sources. I appreciate your reply, if you find it necessary. Thank you! Mr Tan (talk) 12:54, 2 March 2009 (UTC)