I haven't turned on my mining computer in about 1.5 years
Welcome back!
Sounds like you have been living in the woods for a while. Was funny to read your post!
So all you need to secure your investment is the private keys of the protoshares address you had protoshares at (1) before Feb 28th 2014 and (2) after that. I assume you didn't donate to angel shares... If you donated to Angelshares you need to private keys form which you donated.
The challenge is to get your private keys from your compromised computer into a clean machine where you can install the bitshares client (bitshares.org -> downloads). Others are better security experts. I would encrypt the private keys and upload them to dropbox or so.
You own a st(e)ake in Bitshares Play, Bitshares Music, Devshares, and BitShares (main DAC).