Did you plastigauge the bearings to check clearance? Did you check crank end-play and rod side-clearance?
For the timing cover, you can either re-mark the balancer, get an adjustable timing tab that will let you line it up with the balancer mark, or get a balancer that lines up with the new tab.
If you don't want to spring for new lifters, do the cam break-in again. You may get lucky and not ruin the camshaft. Motor oil will run off the lobes before you fire it. Use the red cam break-in lube from Sealed Power (napa) or Comp Cams. Did the head shop set the springs up for the cam you're using? You're running a chevy adjustable valvetrain, right? Adjust until you can just turn the pushrods by hand. Or if you adjust valves before installing intake, adjust for about .050" of lifter preload on the base circle of the cam.
Did you make sure to stagger the ring end-gaps when you installed the pistons?
