I get the HD error as well, but roll as if it were the correct D8, rather than the displayed D10, or whatever. So even though it displays every level as D10 (after taking Fighter levels), the Rogue|Druid levels never have a value entered beyond 8.
This would be more of an issue, if you were using either maximum or averaged hit points per level; even then, you could use the hit point adjustment to "fix" this.
Sphere Caster Level is an adjustment included by TheIronGolem. For the moment, I'm also using this adjustment to fix things.