Based on the photos, I'd cut the gaps out and re-glue it. Probably less work than trying to patch, and the best odds of having it look the way you want it to.

 

Or glue and sawdust the piss out of it

 

I'm sorry, but perfection should have been thought of before you got this far. Instead of just grabbing boards, clamps and glue, measuring and squaring would have been beneficial. ................ Jerry (in Tucson)

 

I would collect some very fine sawdust of the color wood you are filling the gap next to. A orbital or belt sander with a dust bag attaches is a good way to collect the dust. Then pack as much as you can into the cracks followed by some "thin" CA glue, followed immediately with some medium or thick CA glue until on more will seep in. The thin glue acts as a wicking agent for the thicker glue. After it drys if there are some voids where the glue went below the surface just apply more glue. Sand flush and the cracks will almost disappear.

That said if you are having spaces or cracks in the glue joint like that you need to do a better job of squaring up your wood and clamping it during the glue up. Most of those cracks just should not be there if you did everything correctly. Dry fitting, with clamps will show the problems before applying glue.

 

I would probably put some epoxy into the gaps. Adding a little brown dye to the epoxy to darken it may help hide flaws.

 

@LesB Thanks for the suggestion. I'm not quite sure where the problem occured as I did joint every edge and face and planed every opposite face.

@Lazyman Good idea, didn't think of that.

 

If you want perfection, just start over. Not that much wood. Cut that top up into smaller cutting boards and sell them.