Wow, this sounds super cool!
Can you describe the issue in a bit more detail? a few of those images look pretty good.
When you say alignment, do you mean laterally (x/y) or axially (z)?
Are you doing this with a baseplate attached to something in your sample? What is the whole setup here?
What purpose is the GRIN lens serving here? To get depth into the tree stem past other tissue?
Like I said, this seems pretty neat! Just need to understand a bit more before I'd offer advice.