I thought it may have had something to do with the APFS conversion, as well, but the most noticeable difference I had was turning off FV. These noticeable issues happened to me twice on a MBP mid-2014 DG and current MBP mid-2015 DG. All of the anomalies, but not many, seemed to occur after updating with FV enabled. The most noticeable glitches were when I updated on the mid-2015 from 10.12 to 10.13 which is the JHFS+ to APFS conversion. Either way, it's no coincidence to me that disabling FV and then going through the repairs I've noted before ended up being the solution. Twice I've disabled FV with the problems being resolved and re-enabling didn't have the random glitches to reoccur. Without actually timing it, I did notice boot times and commonly used apps seemed to take a slightly longer time but not a great number of seconds difference and definitely not minutes. So, if anyone has time, then disable FV, perform some OS housekeeping, then after about a day or two; renable FV to determine if the problem returns. I'm curious to know if others can confirm that this appears to be a FV problem which I believe happens during or after OS updates and/or patches.
I may do this if I find the time, just to see if I can confirm it before wiping and starting over.