So I ended up taking the bike to my LBS. the dust cover wasn't sitting quite right, so the LBS cut the steerer a bit to allow the cap to fit in snug.

As for the handlebars, they tried to tighten them down a bit but were unable to do any better than i had. They said they thought the screws were the wrong length, since the turned and turned and the bolts were "bottoming-out". They suggested perhaps the seller i purchased them from sent the wrong hardware.

I contacted the seller online and he assured me that the stem was NOS and that the bag it shipped in (with 3T logo and owner's manual) was only opened to insure that everything was padded for shipping.

After examining the newly tightened stem, this morning, i am thinking that maybe the bolts for the stem attaching and the faceplate may have somehow gotten switched up. It looks like the top stem bolt in screwed further in than the bottom one [Check out top photo above]. This sorta seems to be the symptom on the faceplate as well. It seems like there is a smaller gap on the underside of the stem than on top.

The stem shipped with all of the bolts screwed in, so i assumed the hardware was attached in the correct place. It never really occurred to me that the two bolt sizes could be interchangeable. And i am surprised that the LBS wouldn't have thought that that coulda been an option/cause of the problem

I guess i will have to take the whole thing apart tonight. I guess i just wanted to see if anyone who had a Mutant stem had ever run into this and/or if this was a plausible possibility.

Lemme know what you think. Thanks again for all your help above.