I was right there with you last year!
It seemed that I spent the entire period trying to catch the kids up on their assignments from their classes that it was a struggle to actually find the time to work on their goals and improve their skill levels. This is what Ifinally did to help:
1) weekly grade checks, requiring parent/teacher signatures for class grades below a C and what they could do about their grades (turn in work late, re-take quizzes, study more, etc.)This put the ownership of the grades on the students, parents, and teachers.
2) communicating regularily with core teachers to make sure that the work was being modified and the kids needs were being met.
3) writing goals to work within the confines I had to work in so I could effectively work on goals and class work at the same time (reading goals: work on context clues and strategies to enable student X to understand grade level material. In middle school, reading goals were transitioned from learning to read better to using strategies to help understand the grade level material. I had many students who scored a 5th/6th grade level in reading who were able to comprehend 8th and 9th grade material by working on vocabulary skills, context clues, and stopping frequently to re-read,think it through, discuss the material etc. Math goals were more difficult, if you don't understand Algebra, chances are you won't pass Algebra II either.
It was a struggle, and I don't feel that it worked well for those who weren't able to comprehend the material when it was presented orally, but for those who had a single disability (reading comprehension, writing skills, etc.) and were otherwise cognitvely able to comprehend the material it seemed to work.