My image speaks mostly for itself but I will elaborate more in text.
Eastern Indonesia: I switched things around and added where I think some later cash crops should spawn. This will create some desirable city spots in Timor/Flores and western New Guinea, and make the Moluccas not
as much an obvious choice.
Gold: moved to Sulawesi from New Guinea, because as far as I've read there seems to have been gold there at one point.
Spices: replaced the incense in Timor because it's right in the spice islands area where Portugal and the Netherlands will fight in, maybe the incense can be moved to Java or Sumatra?
Pearls: moved from Moluccas to Aru because I found a reference to pearling in Aru's waters but not for anywhere in the Moluccas. I could have overlooked it though, there's a lot of islands in the Moluccas.
Coffee: Coffee is a big-time crop in both Timor and the Flores islands, so you could have it spawn in the 19th century on either tile.
Tobacco: Aru island grows tobacco as a cash crop these days, it could spawn in the 19th century
Whales: I didn't change the whales, I did some digging and found out they do actually hunt pilot whales in that area. Fun fact!
Rubber: It's not on the map but Indonesia became a major source of rubber by the 20th century, I don't know if it's scripted to spawn or not?
New Guinea: An underrated island full of resources, wildlife, and interesting human cultures, but sadly not historically relevant... But I made changes here to open some new viable colony spots.
Pig: Like the picture says, pigs are an important food on this island, if not overly abundant, I thought they were worth adding. Also I changed their tile to a hill so you don't have too much food.
Cotton: German settlers on New Britain/New Pomerania brought cotton at the end of the 19th century, the only reference to gems I found on the island were possible crystal deposits far inland, about 1S and 1E of the copper (under the peak). I decided to replace the gems with cotton here.
Rainforest: This will let you found Rabaul, could be nice if you're playing as Britain, Germany, or Japan. It'll give you a choice between Rabaul and grabbing the copper on Bougainville (I think that's the island that tiles is supposed to represent) or Port Morseby and... uh, nothing really. Hmm, this needs some more work.
Mamberamo river: It's a pretty big river on the island, why not include it?
Other resources: New Guinea produces coffee, rubber, seafood, and sweet potatoes too, but I didn't really want to add these because it might make the island too strong, when historically it was very isolated until the last half-century.
In conclusion this opens up a few new competing city spots on New Guinea. You have Rabaul and Port Morseby in the east, and in the west you can have Jayapura on the copper (or 1W of the copper), a city 1E of the sugar, or a city 1N of the sugar, or a city ON the sugar... You've got options now!
