In the LA engines, the slot in the intermediate shaft should draw a straight line to the farthest forward bolt on the drivers side of the intake manifold. The engine must be on TDC for the #1 cylinder, and both valves should be closed. If the valves are not closed, you are on the wrong TDC, and need to rotate the engine one revolution. TDC should be verified with a check of the piston if there is any doubt as to the accuracy of the damper.
Drop the distributor in with the rotor tip aimed at the front bolt on the manifold, just as the slot was lined up. This will put everything at TDC, firing #1 cylinder.
I've had several engines that just didn't run right when the distributor was not properly aligned. The worst was a Ford 360 that either wouldn't start or wouldn't run at 3500+ RPM.