You are not alone. The school where I work serves a state correctional system and we seem to have more than our share of students with disabilities, including learning disability. To me motivation is crucial. Without it, everyone's time is wasted and teachers end up teaching the exact opposite message than what they want. To motivate our students, we had to design a whole different way of education that may not be possible in a traditional school setting, but I can tell what works for us.
1. Close personal trusting relationships between a student and a teacher.
2. Course credit requirements based on completion of specific assignments, i.e. like a college syllabus defines course requirements.
3. Feedback systems in place that report progress as a student moves through a course and through a diploma program.
4. Remove the requirement for seat time and allow students to move more quickly (or slowly) as they become more (or less) motivated.
5. Students form their own educational goals. You can lead a horse to water... A book you might find informative about this is Summerhill School, by A.S. Neill.
In summary, individualized self-paced learning with explicit course requirements and tangible markers for students to see their progress. I would also like to say that when a school can do this, it will discover there is nothing special about special education. It's all regular education and ALL students get what they need to be successful.