Hi Michael,

To directly answer your question, no, sequential mode does not have the ability to import a ray bundle.  You can use the ZOS-API to define this custom bundle of rays with either a CreateNormUnpol (normalized with Hx/Hy) or CreateDirectUnpol (XYZ & LMN direction cosines).  Both of these will allow you to get all the information for geometric ray trace and you can recreate all geometric analysis with very little effort.  The CreateNormUnpol will also provide the wavefront map in the Exit Pupil, so you can relatively easy recreate the FFT diffraction calculations but the Huygens diffraction calculations become a little more difficult. 

Since you have the wavefront, you can model this in the Entrance Pupil of the system to perturb the incoming wavefront.  Since sequential only traces rays from left to right, you will need to completely reverse your system; there are about 6 steps (more than just clicking the Reverse Elements tool in the LDE) and this article covers the steps: How to reverse an optical system – Knowledgebase (zemax.com).

P.S. if any Zemax engineers or product managers are reading this, having the ability to import a custom bundle of rays in sequential mode to use in any sequential analysis would be a game changer.  If I can pre-process the correct bundle of rays to by pass Ray Aiming but still use the native analysis, this would greatly expand the capabilities of custom tools.