It looks like the height of the X rail above the top skin (the bed) is too short. Looking at how my router will mount and figuring the height of a spoilboard and length of a cutter, and I think I should stretch sides by at least 1". In other words, the right inner skin should go from 9" to 10" or more, with everything else stretching to match. If I go with the stock dimensions, I might have 3" or less of usable Z axis travel. That would be enough 95% of the time for me, but it would be nice to have a bit more.
Has anyone else made this mod? Anyone with a completed machine had a problem with the limited Z travel?
Yes, depending on tool length and spoilboard thickness, it can eat into the useable Z travel by up to a couple of inches. With my own typical setup, I end up with around 3.5" of Z. It always feels a bit strange when I'm using a very small end mill, and suddenly I gain an extra inch or more of Z travel.
The next revision of the plans will actually do exactly what you are describing: raising the sides by a little over an inch. The downside to doing this is that when you have work that is down close to the bed, like cutting simple 2 1/2d profiles out of thin flat stock, the router is hanging farther down below the gantry. This gives it a longer moment arm, and it could potentially cause issues like chatter if you are cutting something hard like aluminum. I think raising the sides is a good mod, and I would go ahead with it, but you might want to think about installing a thicker spoilboard if most of your work needs less than the full Z travel. This will keep things more rigid. The spoilboard could be built up in layers that would allow you to quickly remove some thickness on the occasions when you need full Z travel.