Moon Nicaragua.

You don't really need a rental a car in Nicaragua for the south, Granada, Ometepe, Leon, Rio San Juan/El Castillo, though southern pacific beaches it makes a life a lot easier. For the north, like Estelli, then a rental makes sense. Otherwise, taxi hire from pint A to point B is more economical a less hassle.

Moon Nicaragua.

You don't really need a rental a car in Nicaragua for the south, Granada, Ometepe, Leon, Rio San Juan/El Castillo, though southern pacific beaches it makes a life a lot easier. For the north, like Estelli, then a rental makes sense. Otherwise, taxi hire from pint A to point B is more economical a less hassle.

I understand Semana Santa is busy. We just got back last week from Omotepe. We had a car and ended up not taking it over-we left it in a secure parking at the port for cheap. We could not get a spot on any of the ferries for that day. We had tried to get a reservation by phone but that went nowhere. My impression is the way the system works best is to arrive early and start looking for a spot on a ferry. I did not see any people not get on a ferry. Pretty much everyone got out right away- a spot with a vehicle is different.

It is doable but I would also replace SJDS with Las Penitas. Las Penitas is a fishing village with a nice beach and fun waves. You can of course take a surf lesson but you can also go horseback riding and you can go kayaking in the nature reserve (and go on a sea turtle tour in season). You don't say if you can actually stay longer than 10 days. If you can, I would. Leon also has volcano Telica which is amazing too. The overnight camping trip takes 1.5 days but there are also sunset tours.

Two days Ometepe is not bad but three would be better. The good news is that you don't need 2 days for Granada. You could see Granada day 7 and go to volcano Masaya at night, day 8 do an early (sunrise?) kayak or boat tour of the isletas, then go to Laguna de Apoyo or volcano Mombacho. But if you are hiking up Maderas (tough muddy hike but beautiful cloud forest) you might want to skip Mombacho (cloud forest as well but also nice views of Granada if not clouded).

Although Ometepe is indeed 6-7 hours from Leon by minibus/ bus/ boat I think I would still choose Ometepe. I liked hiking up both volcanoes. Both are tough. They are very different. Concepcion is active and Maderas has cloud forest. You would have to pick one. You can also hike to the viewpoint if you don't want to go all the way to the top. I like the rural life, the beaches, the wildlife. The waterfall hike was fun. Ojo de Agua is great for swimming, relaxing and you might see wildlife. You can go kayaking. There is great ziplining (Chico Largo Adventure): two local guys who are very friendly and make it fun. Great views as well. I like seeing the volcanoes from different angles and just watching people go about their lives.

I liked El Tisey near Esteli. Miraflor was okay but if I went back I would do a homestay. Our friends enjoyed the Somoto Canyon. In Matagalpa we hiked up Cerro Apante and we went to Selva Negra where we hiked in the cloud forest. The trails were nice but we did not see much wildlife (just unlucky, I guess). We took the bus to Jinotega and walked up to the cross. But for longer hikes you would indeed need a guide which could be expensive.

It looks like you will see and do a lot. It is rushed of course (only one full day for Leon, Ometepe, Monteverde, Arenal...) and I wish they had added the San Juan del Sur days somewhere else. I also did not see any mention of volcano Cerro Negro near Leon which is weird. I would choose Cerro Negro or Telica but you also want to see the city.

A full day for Antigua is fine. I would focus on seeing Las Capuchinas, La Recoleccion, the cathedral ruins, La Merced... and the markets. And just enjoy wandering around.

So yes, I would definitely go to Lake Atitlan then March 11. You can at least enjoy the lake from 9 am to 4 pm and that is better than to not see it at all if you are not going to go back to Guatemala any time soon. But hoping you will go back... you can easily spend a month in Guatemala.

In Leon, as you will have half days, apart from exploring the city there is of course volcano Cerro Negro (short hike up, active crater, great views, board or run down). I also love volcano Telica. There are overnight tours but maybe you can wait till you have time for the 1.5 days overnight camping trip. It is amazing. And there is Las Penitas of course: a fishing village only 25 minutes from Leon. Nice beach, fun waves (swimming might be out but playing in the waves is fun) and a nature reserve where you can go kayaking.

I like the northern highlands. Go to Esteli for nature reserve El Tisey. We stayed overnight at Eco-Posada Tisey. There is a viewpoint and a pine forest. Lots of birds. And you can walk to natural reserve La Garnacha. There is also a waterfall: https://treehuggers.cafeluzyluna.org/2017/01/02/tisey/

There is also Miraflor, an agricultural cooperative with canyons and valleys and pockets of forest and at the highest point cloud forest. We stayed overnight there as well. We didn't choose a homestay but I wish we had and it sounds like you would enjoy that: https://treehuggers.cafeluzyluna.org/2016/11/14/miraflor-reserve/

And there is the Somoto Canyon: https://www.somotocanyontours.org/

Matagalpa is a nice town with a cathedral and a few churches. Two parks. Coffee museum. Cowboys. Mountainous scenery (not really high mountains). Coffee farms. Bird watching. Hiking. We liked the hike up Cerro Apante. Selva Negra is a coffee farm, and has cloud forest, trails and wildlife. Jinotega is a small laid-back town with a cowboy feel to it. We liked the cemetery and the hike to the cross. You would probably be interested in this as well: http://www.tourism.ucasanramon.com/index.php/2012-03-06-18-05-05

I like Ometepe so if you still have time that could be another good spot. Don't miss Charco Verde: nice beach, nature trail (easy walk and you can see monkeys and birds, best at dawn or dusk), butterfly place. Ojo de Agua is nice too: a scenic natural spring pool. In/near Balgue you can see petroglyphs, do a coffee tour and/or walk at the base of volcano Maderas. You can also go kayaking. Horseback riding. Hike to the San Ramon waterfall. Of course Ometepe also has two volcanoes. Concepcion is active, Maderas has cloud forest and both are tough climbs. We stayed in Balgue and liked it. Homestays are possible too:
http://www.puestadelsol.org/index.php
http://www.losramos.org/

I have just come back home after a trip to Los Guatuzos (end of April 2018).
For sure land border crossing is very near and is possible (at least for locals) between Los Guatuzos and Costa Rica: when we were in Los Guatuzos, a local "festival" took place there (Nicaragua side), with several temporary food stalls and plastic toy booths owned by people from Costa Rica. Participants were mainly locals from Costa Rica. There was even a wood arena built on purpose for young bull rodeo: I paid show entrance in Nica cordoba, and got change in CR colon!
CR people arrived and left every hour or so with their car (CR number plate) or motorbike, through a gravel road.
So crossing the border there is not a question: the real question is whether foreigners are allowed to cross.

Another (pricey) solution would be to cross border at Peñas Blancas. We arrived in Los Guatuzos from Ometepe island, but on a quite unfrequent and undocumented itinerary:
- we hired a private taxi from San Jorge/Rivas to Sapoa and all the way to Colon (small village on the south bank of Lake Nicaragua, at the end of the road) (about 1.5 hour-2 hours). Cabañas Caiman proposed to book a taxi for us in advance for 150 USD, but once in Ometepe our local hotel could hire a cheaper taxi for us (60 USD). I suppose such a difference may be explained mostly because Cabañas Caiman had planned a large 4WD taxi (we are a 5-people family), whereas we booked a normal 2WD one (4 seats, my wife had the little one on her knees). Part of the road is a good paved road (western end), (central) part of the road is a gravel road under heavy work (paving?) but can be driven with a normal 2WD car without any problem , small part of the road (eastern end) is sometimes in bad condition but still passable with a normal 2WD car (unless it rains). As Cabañas Caiman had warned us, we met 3 military checkpoints: each time, soldiers inspected carefully our passports and stamps, and asked for a sheet of paper with a list of our names, given names, DoB, country and passport numbers.
- then we hired a private boat from Colon to Los Guatuzos (about 2 hours). Cabañas Caiman organized this part well in advance and asked for 150 USD. Since Colon is such a small and remote village, with absolutely no tourist or any visitor spot and no tourist infrastructure, I suppose this private boat does not park in Colon, boat captain probably lives in Los Guatuzos or Solentiname or even San Carlos (hence the price).
Reading Cabañas Caiman tourist register on our arrival ("Coming from:" column), it seems several other visitors did the same a few weeks/months ago.

We did it this way, so I suppose reverse way is also possible!