Okay, so I think I've got the delay sorted out. Here's what I found and cleaned up to fix the problem, in case other people run into this issue.
I observed that, indeed as noted above by Chrisbee, only items that triggered the score motor were experiencing the delay. Spinners, 10 pt shots, etc were all fine. I did some observing with the playfield up, hitting targets that Advanced the bonus. When a switch was triggered, the proper relay would pull, but the score motor would take about .5 to 1 second to do it's thing and rotate. After the score motor stopped, I noticed on the outer edge that a piece (the armature) would very slowly drift away from the sore motor and return to a starting position. Reading over the section on score motors on pinrepair.com, I realized that this was likely my problem.
The armature, which rests against a spring, is pulled towards the score motor during it's cycle, allowing it engage to the gearbox and get things moving. When the motor shuts off, it's supposed to push back to its resting position (the small spring sends it back out). In my case, it was gunked up and sluggish, so it would pull in slower than it should, and also release slower than it should.
Since the armature was slow to pull in and engage, the score motor would be delayed, preventing things from registering as quickly and scoring. Now that I've cleaned it, things are working much better. I may replace that little spring too, we'll see.
For reference... here are some pics.
Score_Motor_Armature (resized).jpg
Score_Motor_Armature_in (resized).jpg