Roof baskets will be very easy. My wife's Jeep has the
Rage Products - Black Widow basket and we're happy with it.
Quick check on the web I wasn't able to find any kits or forum threads where someone has done a custom lift. Doesn't mean that it's not possible.
Will you be working on this yourself? Having a shop play till you find the solution that works best for you would get expensive.
Since your vehicle is older, the first thing I'd do is install new struts and springs. Most coil springs do sag with time and fresh suspension will give you a good base line.
Most independent suspension vehicle seem to be able about 2" of lift, but it would be wise not to start there. While not the most favored, the easiest method to achieve lift would be by adding spacer plates above the strut mounting plate. Whatever thickness spacer plate will be doubled at the axle, so 1/4" spacer plate will result in 1/2" of lift, 1/2" plate = 1" lift and so on. Using spacer plates may require replacing the studs in the mounting plates with longer ones.
Lifting with springs and longer struts would be the most ideal, I currently don't know if any exist that fit the Highlander though.
In my quick search I wasn't able to find bump stops for the Highlander, but they will need to be addressed. Don't want to destroy the struts by bottoming them out.
Another thing to think about is wheel camber, as the top of the wheels will angle out some, positive camber. From what I see a cam bolt is used to adjust camber. Depending on lift the stock bolt may not be enough to bring camber back into spec and custom parts would have to be made.
While there are some naysayers, Firestone's lifetime alignments are very helpful. With my wife's Liberty we've changed suspension set ups a few times and have had no problem getting the alignments done. Think we've had her Jeep done 6-7 times in the 4 years we've had the service. They know we do our own wrenching and if I'm not BSing with the tech the whole time, I'm out in the shop once or twice while the vehicle is on the machine.