...My daughter's FJ40 project is no longer original, so I think we are going to work in some subtle modifications.
What mods do you love?
For a daughter to drive, disc brakes on all four wheels would be the first thing I would do (have done this on mine and love it).
Some will probably say power steering, but mine is still manual steering and my wife and girls drive it, plus I have taught several other teenage girls (friends of the family) to drive in my 40, and they've all done fine with manual steering.
One thing that makes mine so easy to learn to drive in is the H41 transmission with its 5:1 1st gear; it's so low that it's hard to stall it when they're first learning to drive a stick. I put in the H41 for wheeling though; it may not be worth the coin to you just to make it easier for your daughter to drive, but I thought I'd throw it out there anyway. The H41 and Orion 4:1 transfer case are definitely in the "mods I love" category.
If she's going to be driving it at night, I would upgrade the instrument cluster lighting, so she can actually see the gauges. I used a kit from mud member amaurer in mine, that uses electroluminescent wire for this purpose:
For safety's sake, I would consider a good roll cage. I used a MetalTech "Jackson" cage in mine that retains the stock look but adds A pillars and a full cage for the front:
Again for safety's sake, consider some upgraded tail lights. I used these LED ones from Australia that look stock but are about 100X brighter:
Again for safety, I upgraded my headlights with a new harness and Roundeyes lights. A major improvement over stock.
I've done a number of other mods to mine, but these are the ones I would recommend for a daughter to drive.