PhD student leaving current program for reasons of safety. Recommendations for what to do next in terms of schools and catching up? I am a PhD student who lost a year in school due to factors beyond my control. 

First, several non-school related issues made it difficult for me to focus on school. Then, a little later, I was harassed and threatened by someone in my program. The harassment continued for a couple of months before I ceased leaving my house altogether. Eventually I talked to the graduate supervisor about the situation. They agreed that it might be best for me to leave for a while. But, I am left with two problems: 


Most deadlines for schools have past. The ones that haven't, don't seem like a good bet by way of funding. Should I try to find a program to apply to anyway? If not, what can I do to get my year back? I was kind of on a roll before, but now my thought processes feel stagnant and slow — Any recommendations for getting back up to speed? 
My grades from this year are poor. I do not think they accurately reflect my academic potential or my understanding of the material. Should I be explaining any of the extenuating circumstances to prospective schools when I do apply?
I think the department is 'on the hook' to do more than just vouch for you (whatever that means). Sit down with your advisor and the graduate supervisor. Work with them to identify programs which would be a good match for your research plans and with which they or other department members have strong ties. They should be working their networks to help you transfer as easily as possible. 

If you're only a year in, you might also want to think about whether you want to cleanly start over at the new university--retake any classes, etc. as opposed to trying to get credit for any classes you passed in your current program. Were you accepted to other programs before? See if one of those are still a good match.

I know you want to move for various reasons, and you may not want to do anything with the person who harassed you. However, if that person is not getting punished, counseled, or something, the problem is likely to recur with someone else. Ask the department to do something, if only to require the person to undergo a psychological evaluation.