It's been a long while since I looked at Indonesia, and so you probably know a little more about this topic than I do. Looking over the available articles though, I wouldn't say there'd be much radical change from OTL.
There might be some minor changes in the way the CAZ is treated by the Dutch government. Doubtless the West Irian conflict would discursively highlight the plight of the exiled Moluccans, and accelerate decision-making over their eventual fate within the Netherlands. This would bring forward their legal assimilation into Dutch society into the mid-1960s, rather than the 1970s. I wouldn't think they'd have a future in West Papua, really.
As for the cause of the RMS, I wouldn't think Amsterdam would risk further complications in supporting them. The cost of a settlement between the Netherlands and Indonesia might well be the expulsion and cutting of any ties with this so-called RMS 'government in exile.' I would guess that Amsterdam would just want to move forward and minimise all risk of alienating Jakarta and Washington - who don't really want another conflict of this nature randomly erupting - by doing so.
EDIT: Without bumping necessarily, I'd like to also propose a small retcon to chapter XVI. In the section detailing the election of Gerald Ford as Speaker, I said that Leslie C. Arends was one of the 'Young Turks' responsible for his ascension to the dais. He could not be: I made him Secretary for Agriculture in Chapter II. If I could edit the chapter I would cut his name out of XVI, but since I can't, I'll just ask anyone reading to ignore his inclusion in that chapter.