Nice looking truck.
Strange you are having issues with such a small amount of lift.
I ran SPC UCA on my 5th 4Runner so it drove well with 2.5
If I were in your shoes I'd bring it to Toyota and have them align it, if that wasn't who did it in the first place.
Gotcha. Same truck can be sightly different even with same leveling kit. Does it not drive to your liking post alignment? Did you margins all end up in the green?