Pulley alignment issue

[Joe7232]

I know the community is full of much more experienced people than I, and after hours of trial and error i think i need some more guidance. My crankshaft pulley and the water pump pulley won't quite lineup. I have a long water pump and appropriate pulleys and the water pump and the alternator line up perfectly. I used the tool to install the balancer on my crate 350 and the balancer sits about 1/2 of an inch from the timing chain cover. My question i guess is my balancer on all the way? is that the reason my pulleys won't line up? Or is there some glaring issue that I have completely looked over?