That's a really interesting exercise BDF. 
I applaude you for using something a lot of people are passionate about to develop your CAD skills.
Because I've been staring at the YF-23/F-23A weapons bays for hours myself (got them printed on the wall), I would like to offer you the following observations.
1. From the unclassified F-23A plan few - left side, the main weapons bay does appear to have such bulkhead preventing you to stack the missiles this way
2. The bay the forward bay door actuators are visible on Cuts J and K and since the way the rear door open the same way, the actuators should look and be positioned similarly.
3. The famous Northrop stacked AMRAAM missile launcher makes practical sense if you have vertical space for at lest 3 missiles, preferably 4. The F-23A weapons bay is a lot shallower than the YF-23 one, so I believe Northrop might have meant to implemented this trapeze launcher instead. [link]http://www.google.com/patents/US6250195[/link] It would have allowed for wider range of weapons to be launched.
4. The bay doors themselves were each capable of mounting 1 AMRAAM toward the opening, which may explain why the middle section of the main bay if deeper.
5. Rather then stacking the missiles vertically as they were on the YF-23, try misaligning the them like on the F-22A. You should be able to fit 4 on the inside of the main bay with extra 2 mounted on the bay doors.
7. I'd be interested to see if fitting 2x 1000lb JDAMs would still allow for any other AMRAAM to be mounted in the bay.
The reason I believe this is the best configuration is failure in any of the trapeze launchers to deploy would not affect the ability to of any of the others to do so.
Good Luck!
