The fluctuation means a problem with a valve not seating properly or valve that is burned or warped. I can hear a valve tapping noise in your video (starts about 0:10 sec.). It's time for a compression check to confirm. I just did a vacuum test on my own engine. Here is the page from my shop manual that interprets the result of the test:
You are right the STFT will replace the LTFT after a given amount of time. IIRC, the LTFT is the adjustment to the tune itself to compensate for fueling issues over a longer period of time. If the STFT is large for a long period of time (whether +/-), the LTFT will be adjusted accordingly. If the LTFT is at +17% and the STFT is steadily at -3%, then after a ...
Replace the MAF sensor. In looking at your freeze frame data, LTFT shouldn't be that high.
Look at Airflow g/s and it should inrange of 3.0 - 4.5.
Since your freeze frame is at 42mph rev motor up to sbout 2500 and airflow g/s should be in range of 12.5 - 18. If either are not in range replace the MAF per Toyota.