There was a search recently about shimming above mud sills. I do not know the particulars of the problem, but the general rule is....You are building the house now...But you have to live with it for years and years presumably. Get it right the first time. Plan...try out..adjust...but when you move on to the next step, try to make sure it is right. If the foundation is a bit crooked, get out the chisel, or get out the cement and perform the correct steps to fill in to the correct level. If the joist is crooked...get another one and re-do it.
When something is a little off, you continue to build on that little mistake until it becomes a really big mistake. Shims tend to collapse under great weight...Take it apart and do it over, or you will regret it in the long run.