I can't speak to your exact dilemma, but I don't think you can go wrong ordering the Rubicon. If you can swing the extra $2K, I doubt you'll be disappointed. Even if I end up replacing all the Rubicon components later, I'm sure I'll get a couple thousand bucks worth of use out of them before they go. The biggest factor for me was the Tcase and lockers. Sure you can add lockers and an Atlas later, but it's going to cost more than two grand. To me, the choice between a Sahara and a Rubicon clearly goes to the Rubicon. A sport vs. Rubicon is a harder choice, because you might come closer to breaking even when you replace the Rubicon components.
When you really think about it, $2000 is $50-60 a month when you finance. Make sure you get exactly what you want, no matter what the model is. If it takes rationalizing, crunching numbers, test drives, whatever, just take your time. There is no point in rushing your decision, especially if you special order. Of course, it's easy for me to say this now, but there were times I weighed the option of buying an 11 on closeout instead of waiting for the 12. In the end, the 2 month wait was not a big deal and I got exactly what I wanted.