Well I brought my car in for service today on 1 recall and 2 issues:
1) safety recall due to front pass. airbag
2) manual trans shifting 1st-2nd and 2nd-3rd
3) bumping noise when driving on rough road

Took the car out with the tech and he said the trans was shifting well and didn't notice any problems. On that issue, I couldn't argue much because since the temps had gotten a little warmer it started shifting better so I missed my window by waiting as long as I did. Theres always next winter though. As for the other issue, he did hear the bumping noise that I was talking about though. They couldn't find any problems when the car was on the lift so it sounds like they are going to replace the upper strut mounts as per the most recent TSB. Hopefully that will cure the bumping noise I've been hearing in the car. Keeping my fingers crossed.

edit: They had kept my car overnight to get the parts installed today. The mechanic told me that when he took out one of the strut mounts the bearing just fell out. With the new mounts the car feels a lot better and no more bump noise!