1) The resources you listed:
-Copper, doesn't exist in the game
-Petroleum, Cajamarca gets 76 levels which is pretty nice
-Timber, most states have a normal amount of Logging Camps
-Fish, every state has a lot of fishing wharves
-Iron Ore, Peru does have 20 iron mines (more if you count Tarapaca)
-Coal, no, definitely not
-Natural gas, not in the game
-Hydro-power, the Andes do give +1 level of Hydroelectric Power Plants
-Gold and silver: Cajamarca, Lima, Arequipa and Ica together have 11 gold levels (and they start with them, unlike most other states). La Paz and Potosi have 20. My understanding is that Bolivia is richer in gold than Peru, is that wrong? If Peru was the more important gold producer during the era, then I could double their gold levels

2) I already reduced the market access penalty for the Andes to 10%, most major mountain ranges are 15%. The Andes and Amazon do not overlap (so you don't get both penalties) and the amazon improvement journal entries let you reduce the penalties from 15% to 5%.
I'm also not sure what mod you're talking about. In this mod, the technologies aren't changed. In my other mod, technologies are changed but you also get market access from ports and most of the Andes states can build ports, so that's taken into account.

3)My understanding is that Banana country starts with Ecuador further north, is that wrong?
I don't think Andes and jungle lend themselves well to large-scale farming, and farm levels are determined based on arable land. Peru doesn't have a whole lot of that.
It does indeed look like I don't have the amazon river trait in any state, so I'll fix that. River modifiers don't necessarily care about how large the river is, but about how important it is economically and how navigable it is.

Thank you for your response, and the part about Copper is weird. Peru and Chile are the largest exporters of the material in the world but their is no representation of copper in the game, yet? .

1. The Peruvian Sol (their currency) was established in 1863; sol means sun (the coin is bright due to its gold contents). Their sol coin is known to have the best quality of gold. Gold has had a huge impact on Peru. The Incas loved gold for religious and ornamental purposes. Their abundance sparked the Spanish greed. The Spanish conquest of the Inca Empire began with Francisco Pizarro and his 200 conquistadors who murdered the Inca emperor and stole the massive ransom. What followed was one of the largest gold siphons in history; the Spanish treasure fleets financed the emergence of both Spain, England, and Holland as major colonial powers; with the latter two pirating said vessels xD. All this gave rise to golds importance in the area we call Peru. I don't know how you wish to implement gold in Peru as I don't know how much gold they minted in Peru during the Victorian era, but before the era and after, gold was found in abundance to an extremity. To this day there is a lot of illegal gold stripping in the Amazon which has accounted for much deforestation (Peru being one of the largest gold exporters). The potential, culture, and history is there for the gold. In comparison to Bolivia, I could not find many sources attributing to Bolivia having more than Peru, at least in production. Just out of curiosity what makes you think they minted more? Bolivia has a lot but their focus has always been silver which gave rise to Potosi, one of the largest South American cities of the 17th century. Bolivia is more known for their silver and tin.

2. Good point, I got mixed up with your other mod. Btw, the larger mod has some discrepancies with mapi. The USA and other capitols have no capitol state mapi bonus and they do not benefit from other state's ports while Great Britain has 109% mapi due to theirs. I also noticed the tech is different for both mods, my bad.

3. Yes, I wish the amazon was represented in game. As for bananas, are you basing its potential production based on the United Fruit Company and the Banana Republics? The countries with access to the Caribbean did make great quantities of it due to exploitation (most notably Costa Rica). But Peru has records of bananas not only coming from Southeast Asia but also from the Pacific much earlier on. Peru has some of the more unique variants of bananas that are known as super foods. Even though they were not really apart of the Banana wars and were never a Banana republic in that regard, they still produced the fruit/herb.

I noticed the inclusion of the Amazon river, you work fast!

1) While Bolivia didn't produce much gold, I also included silver in the gold good. Both gold and silver standards were used around the world, so it makes sense to treat those as a very similar good.
The statistics I have for production in 1897:
Peru 945 kg gold 101997 kg silver,
Bolivia 517 kg gold 255244 kg silver.
Now how do these translate into the game? I think it's fair to give them roughly the same number of gold mines, but I'll reduce Bolivia's a bit, since they have less actual gold.
By the way, the leading producers of gold at that time were South-Africa and Australia with ~100000 kg per year each, so we're not talking about big numbers for either Peru or Bolivia here.

2. Whoa, that's a significant bug! Anchorages were giving 2% market access globally instead of locally. Fixed that now, thanks.
Capitals do not get a market access bonus, only market capitals do, and for the USA that's New York.

3. Bananas require a particular climate for mass production, that's what I'm referring to. It looks like Peru does at least have a few areas with suitable climate, so I'll give Cajamarca a few levels.

1. Historical production of the time according to records has more weight than the actual potential and undiscovered resources for you right? Just trying to clarify, it is your mod. The adjustment seems good though

2. I forgot about the difference between market capitol and country capitol lol

3. Cajamarca produces a ton of bananas to date.

Potential for production does matter, but statistics about known resources that aren't exploited are usually very scarce, while statistics for actual production are more easily available.