I've not used Miracle's product, I'm pretty much stuck on Aquamix's Grout Colorant. They have a few more colors than Miracle, you might find one better suited to your needs. Great product, works as advertised.

I LOVE your house and II would not touch that mortar - it goes nicely with the aged stone look. I would stay in the brown family for roof color to compliment the aged stone look - not a color that is bright or harsh or crisp. The door is too "fancy" for the house and all the trim is too "crisp" white...look in the cream/taupe/earth-tone family. Not navy or black. Shrubs need to go - think subtle English countryside landscaping. I also agree on clapboard, not stucco, for your addition. I can see ivy climbing the walls - but won't suggest that as you can never get rid of it and it is not good for your stone. Looking forward to your transformation.

Generally one wants the grout not to be the same color as the tiles so that the lines look nice. In the pictures, yours looks fine. If you go gray, it'll be a cooler (color temperature) look, and the grid will pop more. As it is, the tiles don't compete with the counter as much. Digging out grout without damaging tiles is a tedious job. You probably don't need to get it all, just enough so that the new grout can grab, but even so... The question is one only you can really answer: Does the current color bother you enough that it's worth the effort and mess to change it. If you've lived with it for a few months and it really bothers you, it might be. After you've lived with it a year and lived through all that time, your kitchen will be full of so much life and memory that you won't even remember it unless someone reminds you.

I actually thought about doing a two-layer grout on my floors. I wanted a very smooth grout so it would be easier to clean. Unsanded grout is smoother so I thought I could put a thin layer of unsanded grout on top of the sanded grout (required for wider grout lines due to shrinkage of unsanded grout). I didn't do this in the end but I still wonder.... That brings me to my response which is a concept since I haven't actually done this. IF your grout hasn't been sealed yet, which it probably has, you might be able to just grout over the lighter grout. Even though your darker grout will be a very thin layer, wouldn't it's pigmentation particles remain in the pores of the lighter grout? If your grout has been sealed, you should be able to remove the sealer with an acid grout cleaner.