I would not shim one side of the handle to even the tips in height on the tree. I would leave the handle level, because that's how it will be held when drawn by hand. I would also only draw it on the tree by pulling on the string where it will be drawn from by the archer... not from the center of the handle.
If you hold and draw it on the tree the same way you will when yiu shoot it, and syncronize the limbs while doing so, it won't matter if one limb stsrts out in front of the other, or whether it looks odd at brace, and won't matter what the resultant brace measurements are in the end... in spite of all that, it will be well tillered, timed, easy and predictable to tune, shoot the arrow perfectly straight away, without handshock, without tiller shifts requiring corrections or flipping the bow end for end, etc.