Most of the 139 follow suit with any other tune-up of the 858 chassis. So Unit 399 webpage is about the best if not ONLY source for the most current information available - aside from forums like this.
But you did ask a question dealing with VR5 and the AM AGC.
This might sound "weird" but it's really made to help balance the signal IF from both the SSB side and the AM side, making them more EQUAL in signal performance - noise floor, and signal meter - as well as SELECTIVITY and SENSITIVITY the AM side has - COMPARED TO - the SSB side.
The SSB side of the receive is considered "full bore" amplification strip design - maximized more for the Detection and then when decoded - heterodyned with the built in IF - which they knew would be noisy.
It's simply for - so when you switched modes, the thing doesn't go deaf...
You set VR5 as more of a personal preference - be lucky you have it, not all chassis have this.
Tune up is pretty straight forward.
Adjust CT1 and VR5 TOGETHER for BEST LINEARITY
of signal amplification 50uV 27.205MHz Signal
with MIC input 50mV 2-tone AF signal
(Listening for clipping distortions and noise level volume)
You do the best compromise between CT1 and VR5
for "same sound" processing
CT1 trims VOLUME for SSB
Change C242 to a HIGHER value if you
have TOO much SSB and not enough AM
Do the opposite with C242 if you have too much AM versus SSB signal.
You adjust DELTA-TUNE to match S-meter results for Volume of TONE
Adjust VR1for S/RF METER results