It looks fine to me. The only major changes are Ecuador, Acre, Paraguay, the War of the Pacific, and the southern part of La Plata.
Well you're wrong:
-As of 1860 Peru has the northern half of Atacama
-Colombia and Venezuala lost big chunks of the amazon to Brazil (Ecuador lost a little bit) in 1905 that are missing on your map.
-Arce Border is wrong, and Ecuador wouldn't gain that lump of Northern Peru till 1880.
-Your missing the land cessitions of Paraguay (1870) and Argentina (1895) to Brazil
-The Ownership of Patagonia is still unsettled yes, but influnce extend much further, this is the time of Chiles townships in the Magellen strait and Argentina pushing down in the mountains where the natives were weaker (if anything you have the bend backwards as they had less near the coast and more near the andes).
I'm not sure what to do regarding the Princely States. They really weren't independent in their own right, yet they did have some autonomy. Perhaps I should do like I did with the Siam-controlled Malay States?
Whatever, maybe give them all one colour or something, but they are very important.
Also, what's simplified in Indonesia?
Everything

. The situation in 1860 is much like the British in india, the Dutch control some areas but most of it is client states. Also the interior of Sumatra is completely uncontroled. Its not until after the 1870s that the Dutch began to consolidate things into a unified administration. Also they did have control of the Moluccas and islands on the Bandu sea (its what they were bloody there for after all).
Well, they did establish Khartoum thirty years prior. However, I did move up the border a bit. Also, I added in that port they had in Eritrea.
Yes but you had them pushing several hundred miles south into mountains and the worst swamp on the planet that they are still only lightly trying for in 1875.
That required a lot of guesswork on my part, mainly due to there not being a lot of timely maps of the area. It didn't help that Russia pushed south another 20 miles each year.
Well Khiva still probably controlled to the level of the Aral sea in 1860 (though its control of the west by the Caspian was very dubious), Kokand reached much further to the north and the Bukhara-Afghani border follow the contour of the highlands with Bukhara having a bulge into mainly what is now Turkmenistan rather than the finger you have it sticking into afghanistan, and they didn't go as far south into afghanistan as you have (though they got a big chunk).
I was more talking about its seeming rebellion from the British crown

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The Russo-Prussian border is still crazily smooth.