Update: It passed DEQ! Since I initially wrote the post, I put some fuel additive in and took it through on my way to work and it passed. I'm super excited because this means I can move on to address some of the other issues without worrying about fixing some emissions thing.

Thanks for the advice on the filters! I'll have to change those. I also need to find a new timing belt cover for the thing. Mine is completely cracked and a giant chunk is missing. I'm not 100% certain, but I would imaging that it's a good idea to have an intact one. I'd also like to install a triple gauge I've had sitting around for awhile. Since I posted, I also found the "Start here" thread so I think I'll be trying to knock out as much from that list as I can. I'll probably start with the new timing belt and general tuneup in addition to your air filter shout.

I'm excited to get cracking as soon as this rain lets up!