You are going to do what... STOP PLAYING PORTUGAL???
Dude you are going to get a CB shield on the province of Malacca, and you can easily whoop those wussy Muslims around with your superior tech, just assault your way through their lands and avoid the attrition. Eeeeeeasy.
You did take Sansibar, and you did get at least one new CoT for your west African or American trade, did you? There's an event that offers you a CB against Oman. Use it!!!!!! Also use whatever opportunity presents itself against Zanj, don't go for provinces, just go for as much gold and TPs as possible and if you feel like it, vassalize them. (I got 1000d for peace from them!!) You'll notice that all those peaceful nations with 5 traders in a rich CoT can be milked for loads of money. Exploit random CB events against weaklings, but avoid bigger nations, your manpower is pretty low and apart from Conquistadors you have few useful leaders.
You should soon become insanely rich and be able to upgrade your trade tech quickly... that's what I'm doing. Also, take those East Indian muslim colonies before they reach 600pop.
Other things... hmm... Sunda and Bali are easy to convert, it's cheap and while it takes a long time, you can just leave 4k troops and won't have to worry about insurrections. Just send a new missionary ASAP, it might take many years but eventually you will succeed. Oh and you really ought to defeat Atjeh and recuce them to 1 province. Claim all islands with TPs, and steal all other TPs.
Stay in an alliance with Spain and no one will bother you for a long time. If the Spanish don't take the Aztecs out, do so yourself. It's not all that important but it will give you some thing to do with all your money.
The key to Portugal's insane wealth is trade. Trade and little else. Spam the world with your TPs, just keep out of Spain's sphere... but if you can, build a colony with fort in the Caribbean as a base.
Your colonial empire can be developed once you get 30-40d per month at 20% slider position. India is very nice, try to integrate those thousands of natives into your colonies. Like all colonial populations they provide no manpower, but they pay taxes, and base taxe values in India are all high, around 7.
Portugal is FUN!!!