Due to the stock exhaust (i hate spelling that word, there shouldn't be an h in there, so exuse me if I forget it a few times...anywho). There should be an indent in the underpart of the car for a Ypipe to fit.

Im upgrading to an Injen SES stright tip cat back TD. (trueduel) Is the 50mm piping going to hang down and be an issue, or should it fit up there nice and tight?

If you are referring to the well known Injen SES rattle, I came up with a fix for it. Though many people say that if you position the exhaust just right while installing, the problem goes away, well not for me. I tried everything, and still the mid-pipe was hitting the cross member. My fix can be found here: https://g35driver.com/forums/intake-exhaust/54965-injen-ses-rattle-fix.html

It hasn't rattled since I applied the fix nearly seven months ago. Hope this helps.

No, but thank you, ill tell the shop about that when they install.

But Is there a clearence issue when its in, its it going to be lower than my stock exhaust?

And what exactly did you buy to fix the rattle (the tubbing?)

The fix consisted of two 2 3/4" hose clamps around the rubber bushings that the hangers are on. They are tight enough that it has lifted the mid-pipe close to an inch above the cross member. So far from driving around today I haven't heard one single rattle.

The hose clamps are tight enough to allow the bushings to raise up more (make them tight), thus allowing the mid-pipe to hang higher above the cross member. Those bushings are what seems to be just very very thick rubber. A friend of mine had this same problem with his Injen SES on his 350Z, he applied the fix, and has been worry free since. Just make sure your installer raises the mid-pipe far enough away from the cross member, or else you will hear the rattle too.