HID's in your fogs would explain why you have the spare plug hanging. The signal to turn on your hid's come only from one plug, the other is left unhooked and tucked away so no biggie there.
I forgot what all the temp sensor works with, just the mirror comes to mind off the top of my head. Have to research it if you are interested, but that is what the sensor in the last pic is.
If the trans was rebuilt 5 years ago, it could be shifted over from a snag in the install. Again it could also be from headers, depending on the brand of headers used. If the previous owner kept the stock exhaust, then the original manifolds and downpipe could easily be put back on. Due to the EGR delete, I'd lean more toward headers but it's still 50/50.
I'm wondering if the rear O2 sensor was removed along with the other stuff. Others can chime in, I am still learning, but removal of the EVAP and EGR won't really gain anything other then cleaning up of the engine bay. When I had my car tuned I left the EVAP in place, but I did have my EGR removed just because I personally did not want hot exhaust gas flowing back through the supercharger. I'm trying to keep the air as cool as possible. My logic may not be correct, but ehh.... LOL It does have to be tuned out or you will throw trouble codes and other then a couple MPG loss on the highway you won't now the difference.
The joints in the fuel rails aren't stock. I've used those unions on my plastic fuel and evap lines. Why they were added, I'm not sure. could be something simple that the previous owner tried to removed the rails, pulled on it to hard and bent them right there. Instead of buying other rails, he fixed them. No big deal I wouldn't think, just something I haven't seen. More pics of the engine bay will give us a better idea.
As for the trans and fluids, it's alllllll greek to me.. LOL I have my fingers crossed mine will hold up for atleast a year with my build.. I'll baby it, uh huhh..

I have heard as many good stories as I have bad with the trans. As for flushes of fluids, I wouldn't use chemical flushes/cleaners when doing fluid changes on higher mileage cars, but that's just my personal preference.