The oiler tube has a spit hole that should point at the intersection of the timing gears. It's more important if the cam has a fiber gear which was used on passenger car engines, as those are more prone to wearing out than the aluminum gear used on the truck engines. The fiber gear runs a little quieter. I've always used an aluminum gear on a rebuild, as the extra durability offsets whatever slight increase in noise there might be. The cover bolts are 1/4-20 thread, so you could substitute regular bolts for the "stovebolts" that give the Chevy six its nickname.
I used to fabricate and sell a crankshaft snout drilling and tapping jig that used a 1 1/4" ID milling machine spacer as a centering device for hardened steel drill bushings, and also served as an alignment jig for installing the timing cover as its OD was the same diameter as the balancer hub. It had a keyway broached into it that allowed it to fit over the crankshaft snout without removing the Woodruff key. Even without the fixture, the cover alignment should be pretty close. You can always leave the cover bolts a little loose, and tighten them once the snout of the balancer enters the seal, before driving it all the way on. It's a bit tricky to do that with the engine in the frame, but not impossible.
Reassembling without finding a definite problem is always worrisome, but you might have "fixed" the problem without actually discovering the root cause. Good luck!
Jerry
