Are the clearances being checked with Plastigage as recommended by
Chevrolet Shop Manual? Another link from the
Shop Manual on assemby instructions. Finding the right shims can sometimes be a problem. The last time I put a 261 together I bought shim stock from McMaster-Carr. If the crankshaft does not rotate easily ( less than about 5 ft-lbf of torque) at the specified torque with the specified bearing clearances, the crankshaft may be bent or the block may need to be align-bored.
I did run into the problem that you describe, back in 1961. The block needed to be align-bored. The 9/16" main bearing cap screws can easily accept 100-110 ft-lbf of torque.
What type of rear main seal is being used? If it is not installed properly it could be causing a drag on the crank.
Hoyt
