Heya Drav,
I am currently in Baños, Ecuador doing the exact same route you are doing. I started in Costa Rica and am working my way down into Peru over the course of 4 months.
I took the boat from Panama to Cartagena. It took 4 days and I must say it was a pretty crappy experience for me. The boat wasnt a sail boat which I was looking forward to, the food promised was amazing but what we got were sandwiches and hot dogs, the boat was constantly breaking down, there werent enough beds, and the owners had an annoying kid on board. BUT, this was just my experience. I had a buddy get on a boat and had a blast. Same route, just a better captain and group. I think it really depends on the people.
Booking the boat trip can be done in Panama City or in Puerto Lindo and Wunderbar, the only real hostel there. I booked mine in Panama City at Hostel Mamallena. There were a varying amount of boats leaving, at different times. Three were leaving the week I was in Panama City. The cost is $375 or so, which should include meals for the 5 days and all fees getting into the countries.
If you can swing it, try just going to San Blas on your own and then flying. You save a bit by doing the boat and it has the potential to be an awesome trip if you get on a great boat, but you definitely run a risk.
However, DONT SKIP COLOMBIA. It is awesome. I spent too much time in Costa Rica, so I only was able to spend about 20 days in Colombia, but I loved it. Taganga is great for scuba diving and it is extremely cheap. I also did the Lost City trek which was totally worth the $220. It is 5 or 6 days, leaving every day. Think of Macchu Picchu with 10 or 15 people a day rather than 500 on the Inca Trail. It was a brutal hike at times, but I had a blast doing it. Cartagena is beautiful. Medellin is packed with attractive women. Getting in between cities, most buses I saw were night buses. Never had a problem on one of the buses. Getting from the north of Colombia to the south will run you probably 45 hours on buses, but obviously spread out. The worst part is getting from Bogota to Quito, which I just did. 31 hours!
You asked about getting to Ecuador by boat. I think it can be done, but the Pacific side isnt as built up as the Caribbean. I have heard of people getting boats, and you can even jump on shipping boats for relatively cheap, but it will be much harder to organize I imagine.
Again, dont skip Colombia and I just left Quito, and so far Ecuador is quite nice as well. If you have any more questions, I will be traveling south and can give more updates.
Ciao!