We're good with her touching I think. Here's what I did:
I read the specs on the KLR250 and her TTR125. The seat height is exactly 2" different. 31.7 vs 33.7. The TTR is modded with stiffer fork and shock springs, the stiffest ones BBR sells, and the sag is set a touch higher than recommended. To me it felt better that way.
I rolled the TTR up on 2x4's, which would bring the stock seat height to within 1/2" of each other. With most of her weight on the bike she's not quite flat footed but close. She said she could ride it fine as is, but if I could get it down an inch or so that would be nice.
Now, here's what I'm thinking/assuming. The KLR250 I would assume is pretty soft sprung. If it's anything like my KLR650 it'll go through half its stroke just sitting on it. Meanwhile the TTR has stiffer springs installed and is currently sitting on almost new knobbies. Also, the seat is going to be softer on the KLR compared to the TTR. Between all of those factors, I think she'll gain at least an inch.
If not I'll start with setting the sag a bit soft and sliding the forks up. If that doesn't work the next decision will be between shaving down the seat or installing lowering links. I would rather find a replacement seat and shave it down for her, but we'll have to make that decision once the bike is in front of us. Another option that I've read about but need to research more is using a KLR650 shock. I've seen that using that shock will lower the rear about 1". I need to research that option more and see what that does to the spring rate. Might not be the right option for her, I don't know yet. I do like the easy adjustability of the 650 shock. It makes it nice being able to set preload with a socket in 10 seconds if I have a load on the bike.
I've been recommended an xt225, it's an option but I think she would prefer the KLR. Correct me if I'm wrong, but the basic idea I've got is that the xt is a bit better off road, klr on. The planned use of the bike is more 'adventure touring' than trail riding. No cross country excursions, but longer day and weekend trips. She get nervous on the TTR in trails, so I'm sure that either the KLR or the XT would be even worse. She likes riding the very easy stuff, and to be honest there isn't much of that here in Ohio. For true day of trail riding I typically haul my bike there, so it's just as easy to haul her TTR.