Fixing Uneven Sanding After Beginning the Finishing Process

[locrian.vii]

Hi all,
I bought a kit from Pitbull back in November and have been slowly working on it in between work trips.
This is my first kit, let alone woodworking project of any kind.

When I started, I read that the purpose of sanding the guitar was to remove any uneven-ness in the wood, so I spent a lot of time sanding out blemishes from the areas of the wood that appeared obvious to me at the time. What I -didn’t- realize was that by sanding some areas more than others would create an uneven color tone as I began applying the wood stains.

I bought the Cherry Flamenco stain from Wudtone, and after beginning the process it was obvious to me that the wood was taking the stain unevenly. I am wondering if there is any way of evening this out without sanding everything off and starting over. From the Wudtone kit, I have applied the deep color coat and two coats of mixed grain filler and the first coating.

I’ve attached a couple of photos from different angles. You can clearly see the lighter area behind the bridge area.

Is there anything I can do to fix this? If not, it’s no big deal—making mistakes are what first builds are for anyway! =)