Newbie confusion (higher action, digging in, and drop-d tuning)

[TyKao]

I finished a project p-bass. MIM body. Allparts jazz neck. I put a Hipshot Ultralite Xtender key on it. Alignment wise, it's slightly askew so the tuning peg isn't exactly perpindicular to the headstock. I had the guys at NY Guitar and Bass Boutique install threaded inserts (courtesy of Hambone), fit the neck to the pocket, and do a setup. The current strings are .055 to .110 D'Addarios.

Right now, I'm getting a lot of buzzing when I play the 2nd and 3rd frets after slippling the Xtender into Drop-D and using my normal touch. The action right now is pretty normal off-the-shelf Fender action and the other strings are fine. On my starter bass, I have .45 to .105 DR Hi-Beams that play just fine and I don't encounter any buzzing. Then again, I've had those strings on for more than 2 years and they're deader than dead.

I've been trying to apply a lighter touch when I play too, but sometimes I'd like to get the sound of digging into the strings, if nothing else for increased dynamics. As a result, I really don't want to have to baby the strings like I'm a safecracker. Even when I do, I still get buzz occasionally.

I read the Gary Willis and Mr. Gearhead pages, but I'm not sure if I have processed them correctly. I'm really hoping all I have to do is raise the E string saddle. However, since the buzzing is so close to the nut, I suspect it might be a nut issue and I'll have to badger the NY Guitar and Bass people to redo their nut job. What's more likely?

Maybe the problem is something else? Maybe I need to tweak the truss rod a bit? Potentially there's too much neck relief? Is it a result of my less-than-perfect Xtender installation? Do I just need to wait for the strings to die?