Hmm.. If it isn't sitting flush, that sounds like it wasn't put back together exactly, that the place where it came apart isn't meeting together like it should.
If that is the case, the good and bad news is that it is likely to come apart again. Hopefully if that happens, it will be while the spen is out of the phone and it happens when you are aware and you don't lose part or part of it gets stuck in the phone. Since doesn't seem to be back together exactly, if I were you, I would buy one of the less expensive replacements and use that. If you can't do that, then when and if it comes apart, very gently scrape and pick off the glue with a thin, sharp knife. I'm assuming you used super glue. If you can get it all off, and not scrape down any of the actual spen, then you can get it back together exactly and it should hold it well.
To glue it back, at minimum, I would use a very thin layer of the gel super glue. Less is really more with applications of super glue. The most important aspect is getting it lined back up perfectly.
The glue that would probably be better, but is more difficult to work with, is Gorilla glue. If you aren't familiar, it takes a light mist of water to activate and it expands almost like a spray foam does. If you use the Gorilla glue, you need a very, very, very, very, very, VERY thin layer and just a tiny, tiny mist of water before putting the two ends together. Even though I've used Gorilla glue a few times, I would still practice first on a couple of plastic pens that I break in half. That will give you an idea of how much it expands and how much to use. The Gorilla glue can be good if a tiny piece chipped off where you are gluing it back or if the ends are no longer exactly perfect to meet together completely. It can fill those tiny areas and make it strong there instead of it being a weak point. You just can't have too much and you will want to make sure that as the glue expands over the few hours it takes to dry, it doesn't push the two pieces apart any and make it longer than it is supposed to be.