I realize that this is probably banging my head against a brick wall but I do not like to be beaten. I have ignored all previous advice and gone back to the base problem.
Your monolithic audio track is the key - all timing is related to this, so lock it.
Trim each original video clip in the source monitor of Pr to the lexact ength you want to use. Extend each end of the clip by EXACTLY HALF THE LENGTH OF A TRANSITION (you will find life easier if you have all transitions the same length.).
Process your video in AE. Do not alter the length of the clip. Bring it back into Pr.
Open each clip in the source monitor, and trim EXACTLY HALF THE LENGTH OF A TRANSITION from each end of the clip.
Place the trimmed AE clip on the timeline, and synch it with your locked monolithic audio track. Repeat for all clips.
Where these trimmed clips but against one another you can apply a transition, as there is the necessary handle of additional material present for the transition. Doing the trimming away from the timeline avoids any upset to your main audio.