The recommended version of MODTRAN is MODTRAN4.
Yes. For more information, see the related question in make_adb FAQ section of the The make_adb User Manual.
In theory, yes. PLEXUS could be used to create the MODTRAN tape5 template file that is used by the DIRSIG make_adb tool. We are not aware of anyone who has tried this.
Yes, and no. The "adjacency effect" is the contribution of photons that are reflected into the atmosphere by an object of interest near the target, which are then subsequently scattered by the atmosphere toward the sensor. This component of the radiance reaching the sensor appears to have originated at the target, but it is "colored" by the nearby object and the atmosphere that scattered it rather than by the target.
As of version 4, the MODTRAN model supports modeling adjacency using the DISORT multiple-scattering features and addition set of cards in the Card #4 set. To use this method, the user needs to provide the reflectance of the target and the average reflectance of the surround. Using this capability in MODTRAN, the DIRSIG model could incorporate adjacency photons if it called MODTRAN for each pixel. However, this is not computationally tractable since a single run of MODTRAN in this mode can take 10's of minutes. When expanded to millions of pixels, a single DIRSIG simulation would take years.
As a compromise, you can create an atmospheric database for your scene that contains adjacency photons with some compromises. This is accomplished by creating a tape5 file that is setup to model adjacency using the defined MODTRAN procedure. In this MODTRAN input file, supply an estimate of the average scene reflectance as a background reflectance. When the make_adb program creates the atmospheric database the path radiances computed by MODTRAN will include photons from the adjacency effect. The caveat to this approach is that it assumes the reflectance of area around each "pixel" is constant across the image. In some scenes, this may not be the case. For example, a heavily vegetated region that transitions to a rural or urban environment.
This problem is an active area of research and a better solution is under investigation.