Time management and motivation are two of the hardest things for me, and I think for most people.
I am very disorganized. I've tried different software packages to help me, but I can never seem to fit what I am doing into their little boxes. I'm back to using a text file to store ideas and ToDo items.
One important key to motivation is selecting projects that you are really interested in -- stuff you really care about and really like working on.
Of course, that can cause problems for time management.
I try to select projects which will have some value very quickly, and yet be expandable beyond the original scope. That helps me phase my efforts and still maintain motivation. If I have a project that isn't going to be useful to anyone until I've done two years of work on it... it's just not going to get done.
I also mentally divide my tasks into "low hanging fruit" and "big deliverables". I start my morning with low hanging fruit -- tasks which are easy enough to accomplish in under 20 minutes. I try to have one big deliverable before I go to sleep, like "put the tools menu online". That took about four hours of my day yesterday.
Another motivational "trick" I use is summed up in the old saying "A change is as good as a rest." When I get tired of one task, I change to another task. When I get tired of that task, I change back. This works very well to alleviate burnout and maintain performance.