Ma Mopar has used several different BB timing covers over the years and the same on the balancers, they need to be made for each other to align the timing marks correctly
You did good catching this
I have not used a 400 timing cover yet so I can't tell you what is wrong, I have bought several of the cheaper Powerforce plus SFI rated BB balancers that Summit sells to use on Hi Po pump gas street motors recently and they both had two sets of zero timing marks on them, does yours?
As already said to determine exactly where TDC is you need to know exactly where that is, I use a dial indicator on the piston tops in the center of the pistons on most of my builds to degree the cams in and I will occasionally use a piston stop also to verify how close I came to being perfect on the TDC marks on the dampener and timing cover after the balancer is on
I do also use the dial indicator on the #6 piston at TDC before installing the heads to verify the dampener zero mark aligning with the zero mark on the timing cover
IHTHs