UPDATE...(Just realized after more searching that Duhhh! there were 2 diff size bolts for each end so I put it on right). Ive been having misfire issues lately with no CEL or codes!. It started a few days after almost running out of gas. It seemed to get worse as my fuel level dropped. It's mostly during moderate acceleration, but goes away under hard acceleration. It sometimes does it at idle also(2001 a6 2.7t). I decided to change the fuel filter. I drove the car after replacing, and it still seems to be running rough, but not as bad. I followed the proper instructions like running the car for a few seconds without the fuel pump fuse, but I forgot to take the gas cap off.
I'm wondering why it still seems to be running rough,again, it's not as bad as before, but then again, havent taken her on the hwy yet. Also, I tried to blow through the old filter and it was completely blocked. I have not had any trouble starting the car at all. Before I changed the filter, I changed all plugs, and swapped all coil packs with a new one I have, and no change. Could I possibly need to fill it with some fresh fuel and burn out some junk left inside?? any feedback appreciated.

 

The fuel filter arrows should be pointed towards the front, ie same as the fuel flow. There are some other posts on running low on fuel. The filter screen could have gotten partially clogged or if the fuel pump is marginal then running low on fuel can cause it to overheat. And if the filter was totally clogged that could have caused a problem. Have a shop test fuel pressure on the fuel rail.