Pack light. Learn some basic Spanish (just a few phrases make any trip easier and better) and take a phrasebook. I wear a hidden money belt for cash, debit card, credit card and passport and I have a day pack for anything of value (phone, camera) that I keep with me and there is nothing of value in my backpack (so I don't worry if it ends up on top of the bus or in the back of the bus). Ask the locals about safety (for example before going on a hike). Be alert but not paranoid and when in doubt take a taxi or tuk tuk. We get the local currency from ATMs with our debit card (we take some USD in good condition for emergencies). In Belize, Guatemala, Nicaragua, Costa Rica... just go the bus terminal and hop on a bus. The exception could be longer bus rides but even then there is often no need to book in advance. On some legs shuttles are easier but of course more expensive. Shuttles can be booked the day before at a travel agency or through the hostel. In Peru we booked long (overnight) bus rides a few day in advance (we bought tickets at the bus terminal when we arrived somewhere or bought tickets online). In Peru and Colombia domestic flights are cheap and sometimes not much more expensive than taking a bus.
Not to miss (these are the countries I have been to):
In Guatemala: Tikal, Lanquin and Semuc Champey, Nebaj, Xela, Antigua, Lake Atitlan and at least one volcano hike (Acatenango overnight for example).
In Nicaragua: Jiquilillo, Leon + volcano Cerro Negro + volcano Telica overnight, northern highlands, Rio San Juan, Granada, volcano Masaya, Ometepe Island.
In Costa Rica: the Osa and the Caribbean coast (and then from Puerto Viejo to Bocas del Toro, Panama)
In Colombia: Villa de Leyva, Barichara, Tayrona, Cartagena, Jardin, Salento, Tierradentro, San Agustin, a paramo hike
In Peru: the north (Trujillo, Chachapoyas...), Cusco and the Sacred Valley and Machu Picchu, Arequipa and the Colca Canyon and via Lake Titicaca to Bolivia

On my trip I visited Pisco/Paracas, Ica, Nazca before I got to Cuzco. I also did Salkantay trek to MP that took five days. All that took roughly ten days. You can skip that on your trip if you want to save time.

Re Chile.
I finished Salar de Uyuni tour at the Chilean border, so going back through Chile was a good logistic combination.
I spent a couple of days in San Pedro de Atacama and took a night bus to Arica. Spent a night or two there and proceeded to Tacna, and farther on to Arequipa. Spent four days there, visiting Colca Canyon and doing whitewater rafting in Chili river.
Visiting Arequipa was a good route logistically, as I didn't want to go directly from Tacna to Lima. Arequipa itself is a very nice place to visit.
You can redesign your itinerary and do similar to mine, without a few bits that you'd have to sacrifice to fit in your time frame.
The good thing is that you don't need to decide or book anything in advance, and adjust your travel plan as you go.

I am currently in Ecuador and came down from Mexico. As for the onward ticket, I've never heard of this website but what everyone, including me, does is go to copa air website, book and flight but at the end press the pay later option. They then send you an itinerary and you can screen shot it or print it out and show the border control this. You never need to pay or put in a credit card. It's worked for every one I've travelled with across borders. You need it for both Panama and Costa Rica! Otherwise the border control will make you buy a bus ticket at the border to show you will leave. This cost like $30.. if you prefer to do it that way.

There wasn't a real lot of people going up but now I'm in South America a lot of people are heading up to central now.. I think it really depends on the seasons!

Panamá - stay at hospedaje casco viejo. They have a book in reception with literally ever San blas option, it's really helpful. Look into coiba island as well for snorkelling or diving, many people say it's one of the best in Central America. If your looking for something super different head down to Darien. There's indígenas communities there that are amazing to stay with, if you speak Spanish.. it's was the best 2 weeks of my life.

Costa Rica try volunteering maybe? I did that to save money on accomodation and food.. a lot of backpackers also hitch hike and couch surf in Costa Rica because it's so safe. Hitch hiking it's pretty common, I did it a lot with locals when volunteering to get around. Cahuita in my favourite. You can get a cabaña for $20 with kitchenette and just hang out. Manuel Antonio is a must for animals.

Nicaragua - check out volcano telica, it's an overnight treck. It's real easy and there's no barriers so you can literally walk up the the volcán and look over to the lava. San Juan has good parties. In Estelí there is this guy who lives out on a farm and he's spent his whole life carving into the rocks, it's really awesome what's he's created and it's a really interesting guy. If you ask at the tourist agency next to Luna hostel they will tell you how to get to him. Also don't miss the war museum in Leon, you get a tour from the guys who actually fought in the war, it's also a great experience.

Honduras - if reverse you would go Estelí to Tegucigalpa and spend the night there. Do not travel at night even on a tourist shuttle.. too dangerous. Just book a hotel in advance and take a cab. Then from there to la ceiba where you can get a ferry to utila. There are many great hostels in la ceiba if you want to stay a night. From there you then have to pass through San Pedro sula, then Santa rose then copan. Start super early or spend the night in Santa Rosa.. but it's expensive in Santa Rosa.

If you can fit in at least the ruta de las floras in El Salvador. Juyua and atacó at the least. They are beautiful towns.

Guatemala you could add in rio dulce and Livingstone. You can kayak down the river from a lodge to Livingstone. It took us a few hours and was amazing. The lodges then take the kayaks back for you. It's an interesting trip to see the blacks and Mayans living together. Your meet a local guy name Flores. He will start a convo on the street and will invite you to his place to chill and will tell you about the culture and everything. He works with the local school and has a long list of people from around the world that have stayed with him.. some semi famous people too! He speaks English. You should also look into el mirador, a 5 day treck to the biggest Mayan city.

Hi!

ive just returned from 7 months in CA and i can tell you 3 months is nothing! I was there is rainy season and during the hurricane last year and it didnt effect tourism what so ever. there was never a time which i was alone. In Mexico, Guatemala, El Salvador, Honduras, Nicaragua i spent under US$36 a day. days without activities was even less. Costa Rica and Panama US$36 is still doable but i ended up spend around US$45 a day only because i love to eat good food! if your on a budget a tip is in CR and Panama fast food was a saviour. Mcdonalds and Subway both have menu del dia for $3 which was a change when i didnt want chicken and rice for $5. a general rule is i never paid more than $10 a night. only a handful of times in CR or Panama. In Guatemala, Nicaragua, Honduras it should be around $6

Guatemala - spend a few weeks in Lake Atitlan learning spanish. stay in San Pedro for a decent social scene. Check out the Nebaj to todo santos trek. El Mirador trek also super worth it.

El Salvador - Juayua and Ataco and not miss. Stay at Casa Mazeta in Juayua and chat to the owner Darren who will tell you everything you need to know about EL Salvador. Suchitoto is also a beautiful town.

Honduras - Diving and snorkling in Utila.

Nicaragua - From esteli there are multi day hikes in the near by cloud forest. Also there is a man who has spent his whole life carving into the cliff, its worth a visit to see him. ask at the travel agency connected to Luna Hostel. and check out the israeli restaurant next door - hummus, pita, falafel and drink for $3 - best in CA. In Leon check out the war veteran museum, you get a tour by a real veteran and their experiences are amazing. There is also a overnight trek to volcano telica which is awesome. Party in San Juan Del Sur.

CR - Relax on the beach at Samara or Montezuma. Monteverde for some nature and hiking. If your really into animals head down to corcovado for a multi day hike. just be aware it is $80usd a day. Cahuita and Puerto Viejo are little party/beach towns. Manuel Antonio is the best park for animals with heaps of sloths. as mentioned above you will need to provide proof on onward travel. you can buy a bus ticket or use one of the many websites that create fake itineraries which most people do. I just did a fake ticket to another CA county and told the agent i was flying home from there. Crossing into Panama though i was with 3 Austrians and the border guy for some reason told them they had to have a flight to their own country, which was strange but i think that was the exception

Panama - Coiba island has the best snorkelling in CA. Anton valley has a few nice hikes and the hostel there is expensive (16$) but has everything including pool, spa, BBQ, games room. Stay as Hospedaje casco viejo in Panama city which has a whole book of options for San Blas and you can choose the best option for you. I woud also recommend making the journey to the Embera community in Daren (only if you are confident with your spanish). 2 weeks there has to be the best experience of my life. again you will need onward travel for Panama.