I have also experienced this sort of scab formation on the underside of the shaft near the glans (frenulum).
In my case it was for the most part simply a matter of wearing the inner wear for extended periods of time rather than taking more time to rest and recover during the initial conditioning period, which I believe to be the case for you as well.
You clearly have a good handle on things by slowly increasing your wear time and now taking a three day break.
Once you feel you are ready you can start wearing again and be more alert to the irritations that can occur with extended use.
As you get more time in the saddle so to speak these irritations will stop happening as the sensitive skin becomes more accustomed to being in contact with the innerwear on a full time basis.