If you do use a red for the trim, be careful not to choose a bright or purplish one. Use a red from an historic paint palette (the chip will probably look brown). Personally, though, I'd choose something more neutral and natural, maybe a taupe or cream. Red would be a pretty accent color, though, maybe on shutters? Or sage green shutters, they'd pick up the green dormer color nicely and make it seem less like a leftover that predates the vinyl siding. And a second vote here to remove the roofed-gate thingy. It clutters up the front of the house, for resale you might want to get rid of it.

You are correct that both windows probably had the bowed leaded glass windows. Please DO NOT replace the original Greek Revival columns with square ones that will ruin the look of the house. Yes replace that awful metal railing with a wood one. Try to find the appropriate style in architectural salvage places. As for color combos. The creamy yellow for the trim and the green for the fish scales. In fact you can use the way this house was painted as an inspiration.Here's a similar color scheme. Obviously the brick would be the red, but I'd also consider painting the window sashes in a red to match the brick.The cream color Judy G suggested painting the whole house would work, but it's really not authentic to the style and it won't really highlight the beauty of the house. Here's a great article on painting a victorian beauty.

I would use a cedar wash and pressure washer to clean the cedar first to see exactly what shape it's in. You may need to replace some boards. Then remove the bush and tree in front of the house. You can probably find a good used door to replace the current door. I would look for fiberglass for low maintenance. After it's been cleaned and the bushes and satellite dishes removed, post more pics for more suggestions.

Do you have any pictures of the house and where the stone will go? Urbane bronze siding and a black roof will absorb a lot of heat in the summer. Our house is a brown of a similar darkness and it’s hot to the touch in the summer.