Need I worry about intake grommet issue?
 

I have heard stories of a certain grommet from the intake box falling into the fans.

I put on my MS intake and noticed that on the bottom tray where the stock intake box used to sit there may be a missing grommet? Should I worry about this at all?

Well, take a flashlight and look around in the fan area. If you don't see the grommet, then don't fret. Both of my bottom grommets are gone to who knows where, but there is no evidence of them in the fan area. And I don't intend to replace them.

All I should need to take out is the bottom part of the intake tray correct?

^ Yep, a good flashlight will help. I have heard of people saying it gets stuck inside the fan and creates a big cooling problem, so try to make sure you find it!

Then again it may have been missing for a while or fallen to a safe place. Either way, give it a serious try before shrugging it off.