I replaced about 20 fuses and most of what wasn't working is now working. Interestingly, none of the fuses I replaced showed any visible signs of a problem. I haven't yet checked them with a meter. I got the replacement K40 in and installed that, the old one doesn't appear to have any bad or burnt places in it so I have a spare if needed

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I am still getting the rough idle at times, although it seems to be greatly diminished at this point. It's occurred once since I changed out the fuses. At that time I popped the hood and checked for air bubbles but didn't see any. As it seems to be intermittent I'm thinking something along the lines of fuel delivery. Both the fuel filters were just changed. I've read there is a screen that should be checked so I'll look into that. The absence of air bubbles has me thinking the O rings mentioned before are probably ok?
Overall mileage is good I think at 33.5 mpg (i do a lot of highway driving to and from work).
As for what I paid for the car, I got it for around 7K and it was very clean!