Hey Rich,
Couple of questions..
The rod bolts are Torque to Yield type of bolts. Did you reused the bolts and if you did, did you measure the stretch? When you re-torqued them, you need an initial value of around 35 ft lbs. Then you stretch the bolt with an additional 100° turn. If the bolts are not in spec, then you can't get the desired torque.
Second, did you check the end of the oil pump shaft? If you are not certain the knocking was coming from #2, the oil pump shaft along with the helical shaft could be very worn and possibly make the knocking noise.
See pics of an oil pump shaft beginning to wear. Still serviceable for a lot of miles though.
