If I had this problem, I’d have two or three terminal windows open. One to run the rebuild, one to take notes on the elapsed time and to note where the long delays are happening between log updates, and the final one to keep a record of machine activity: probably running vmstat 5
When you hit a point where the log isn’t updating for a suspiciously long time, take a note of the activity reported by vmstat.
Post suitable extracts from the log with your notes and the corresponding vmstat output here.
It seems highly likely that it’s specific parts of the rebuild which are taking time: the thing to do is to find out which parts, and see what the machine is doing at those times.
I’d probably also take a snapshot of machine activity with ps auxf during the pauses too.