Has anyone had issues with check printing formatting? Seemingly simple things like moving lines a few centimeters, centering vendor address for envelope, etc. are eating up a lot of consulting hours. Wondering if this is a common occurence.

Sometimes that can happen if you've got odd check stock that required an advanced PDF. How many hours are you at so far on it? In all honesty - unless you are sitting on thousands of dollars in check stock - it's just better to buy quickbooks supported check stock from another provider (not NS Direct) and then you shouldn't have to change anything.

I think we are in the neighborhood of 50 hours in and it's still not complete

ok, that's a bit ridiculous