I need to know what is meant by setting the register on a rebuild.

I remember doing it in 2009 but forgot where to.

I dont call it that but I think he is saying
to set the #3 main bearing(thrust bearing)
wack the crank shaft back and forth with a
mallet before tightening the cap all the way

Thanks, I did that after we put all the rods in, every thing turned good. I prayed the crank with a big screwdriver back&forth then torqued it, put 1 rod and torqued it spun 1 time, then put another torqued it spun it and so on. Then hit the end with a rubber hammer. Can that be a problem? My friend is coming with a dial indicator it was .007 last time on the same motor & degree the cam.

I like to see between .004 and .010 on new bearings and a decent thrust surface on the crank
I like to see more rod side clearances than a lot of the folks on here do also, .016 + minimum up to .060