Long story short, the entire set of TCK tests that apply to the functionality included must pass the TCK in order to be labeled "certified".
TomEE+ passes the same tests that TomEE passes (more actually), but by virtue that it includes more things and not all of them pass their respective tests, TomEE+ is not certified.
We actually only had one distribution, just plain "TomEE", but for certification requirements it became two, TomEE (the now stripped down version) and TomEE+ (the original).
TomEE+ actually passes the JAX-RS TCK, we run those tests everyday. In order to have a certified binary that includes JAX-RS we would have to either create a third TomEE distro that's Web Profile + JAX-RS, or just add JAX-RS to the plain TomEE binary. We're adding JAX-RS to the Web Profile in JavaEE 7 at the JCP level, so adding JAX-RS to plain TomEE is just a matter of time.
At the moment we're just trying to get the 1.0.0 out the door -- actually took a break from that to come check out stackoverflow :) Neck deep in scanning code and needed a bit of a breather :) The coming 1.0.0 is already about 20% faster on deploy than the released beta-2, but after this round of hacking it should be much more. I dare not say how much till it's finished, but it's looking really great so far.
Anyway, give TomEE+ a try. If for some reason you feel there are still more benefits to putting all the parts together yourself, definitely let us know and we'll figure something out. Our whole deal is making it so you don't have to do that yourself anymore. So if what is up there doesn't quite fit you, we'll make something that does.