all the people i've ever known who have worked for non-profits have these same kind of issues. the organization is low on money, there's little mobility, and if you have a bad boos, you're stuck for a long time.
how long until you graduate? once you do, and you move to a different department within your organization, will you have a different boss (other than your current big boss)?
it makes sense that you're not getting the support you want - your old boss didn't get the support he needed, and the big boss didn't care. now that your old boss has left, i'm sure the new boss wants to see how much money he can save by watching you work yourself to the bone. your withering department is not valuable to the big boss, or you (and your old boss) would have gotten more support.
you have to ask yourself, is this job (not the organization) worth it? If yes, just stick it out until you graduate, perform as best you can with the support you're given, and then transfer out of that withering division. best of luck.