1) Consider a stored boarding ladder like the F-35's.
2) IF you go with a built-in boarding ladder, put the gun on the other side (yeah, I know the F-35A doesn't, but the gun's far enough outboard that it shouldn't matter on that one).
3) YF-23 had a single weapons bay, F-23 proposal had tandem weapons bays with a moveable bulkhead between them (see similar installation on the B-1B); I'd probably go with the lengthened fuselage, myself.
4) Upgrade to two F135 or F136 engines for the FB-23 and stay with two engines. Carefully blended so as to preserve the low RCS, I could see filling in those areas; I'd probably build them up with sheet styrene or cut sprue and only apply putty for the outer surfasces.
5) Using the F-35's EOTS shape would likely get you close enough and, I agree, it would make for more interesting lines. To make it more interesting, something similar in front of the cockpit canopy as a lidar unit?
Further Note: The shorter F-16 pylons would work here as the F-23 wing clearly doesn't have the ground clearance of the F-15 while being a lot closer to that of the F-16.
I've also looked at combining two YF-23 fuselages in 1/72 with the cockpit and nose of a Su-34 for a FB-23 and it looks feasible.