Yay for more Isabela's! I've got some pics in my gallery of Isabela-in-progress, though I'm doing the "romanced" version and making some tweaks here and there. I went with a dress and a corset for mine, though in the game it looks like it's all part of the same dress that's split and attached at the sides.
As for the boots... hoo-boy, they're fun. You could make your own boot covers, if you're comfortable doing that. Isabela's actually kind of look like boot covers sometimes, especially in this pic:
But... I went the lazy route and just found some thigh-high brown boots on eBay. I just kept running searches for "brown thigh boots" until something popped up that would work. Luckily most sellers will list the upper-opening circumference and total boot height, so you can check out your measurements and see which ones would be tallest and fit you best. If you have smaller feet, you should totally check out these for a base:
I would have gone for those, except they don't have them available in my size.
As for the dress... I lucked out and found a cheapo old Gap dress on eBay that was just about perfect. I'm all about buying stuff as close as possible to the end product and then adapting.
I just kept running searches for "white cotton dress" or "white peasant dress" and checking off the options in the side bar to narrow it down to my size.