My builds are among the slowest here. Life tends to interfere with my guitar building. A common issue I think ;-)

At least the filler flattens and sands well even if the color is a bit off. You still have options. My only successful stain job had a number of issues (mostly my mistakes). I had to work pretty hard not to get streaks or blotches...or more accurately to even them out. I had problems with the fill and problems with the initial clear coat as well. This resulted in some light spots where I ended up adding more of the General Finishes dye stain that I was using. Once I got it as flat as I could I used a gel stain (Craftnique) over everything to even out the color a bit more. That went over original stain, clear filler and some clear coat. Once I had everything as even as possible, then I clear coated again.

I am mentioning this because some stains seem to work well over finish, filler, or clear coat. Usually these are not the dyes, but if you can't get the color the way you want with dye stain you might try something else to even it up. I don't necessarily recommend Craftnique, but there are gel stains, and translucent paints that are designed to go over old finishes and filler that might work well. I think there are folks here who have even drawn in "grain" over filler with a sharpy type pen. Worst case scenario you can still add a veneer "cap."