Do not miss a stay in San Pedro La Laguna, Guatemala (but I am sure you've already planned on going there)!
The route in at the eastern side of the lake may not be the easiest way, but it makes for a very interesting ride, and the view coming into the lake is awesome!
Also, when you get to El Salvador, you should visit Conception de Ataco (one of the best places we visited on our trip). It's such a great little town. If you'd like, PM me when you get near there, and a friend we met while we were there might be able to give you a place to stay.