Your picture will only be as good as the glass in front of it, so don't skimp out on filters. No sense in ruining the good camera and lens with a crap filter. The cap will be fine for protecting it. If you want extra protection while using the camera, a hood will help keep it from getting knocked into things.
I don't see anything wrong with the LCD protectors. I don't use them personally, but nothing really is wrong with using them either.
The only other thing I would suggest is some cleaning equipment. A brush, a blower, some cleaning solution, and some wipes. If you are uber-cheap like me, you can use a soft make up brush, and an ear bulb from the pharmacy. You can get both of those together for under three bucks instead of using a lens pen or lens brush and a rocket blower. Then just get some good cleaning solution and some disposable lens wipes and you'll be set.
The only other thing I would suggest is keeping the holster in the other bags if it has camera equipment logos on it. Nothing screams steal me like logos stating I have expensive camera equipment inside, specially while traveling.
Awesome, I like the cheap option

(well, after dropping $600+ for the camera) .. Thanks for the tips, I'll pick these up on the weekend. As far as branding goes on the case, I don't think it has anything on it, but it CLEARLY looks like a camera... In any case it'll be in the top rack pack, which detaches easily and has a shoulder strap - so it will be coming with me everywhere ( my passport will be in there too )... I'll just hope that the actual panniers with cloths in them don't get nicked if I pop up to a touristy location and lock the bike up.. but who wants to steal used cloths anyways. I'll just hope for the best with those.
BTW, I checked out your Facebook page with your wildlife shots - Great stuff! were those done with the d3200?