For context, I installed a new suspension a few weeks ago with some new tires. Bisltein 5100 all around with OEM front springs and Bisltein rear springs, and 285 Wildpeak AT3W. It's now sitting at a 3.25" lift front and 2.5" rear. I also got a shop installed a pair of JBA upper arms due to the 3" lift.

Anyways, I drove the runner for few days and noticed some pulling to the right. So I got an alignment done to fix the issue. Two (2) things I noticed:
1. Steering wheel is slightly off-centered, probably 1 or 2 degrees to the right. It seems like it's driving straight now, maybe just drifts to right more vs a pull. But when I try to straighten the steering wheel it would then drift to the left.
2. Going over 65mph on highways the handling becomes less stable. The steering wheel feels a bit drifty. Meaning I have to concentrate on holding and controlling the steering wheel. Although it's not bad on short rides, I imagine it could become exhausting on longer drives.

I'm likely gonna go back to the alignment shop for them to make some adjustments but I just want to make sure I know my demands before going in there. So here are my questions:

1. To straighten the steering wheel, do I just need to make a small adjustment to the tire position or would I risk messing up the toe alignment?
2. What needs to be adjusted to make the handling better? Will it help if the caster is set to higher deg, 3-4 deg?

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Sounds like you need a panhard correction kit.

Bolt-On Trackbar Correction Kit (BOTCK) For The 5th Gen 4Runner

Ah TIL about panhard/trackbar. After doing more research on this, I feel like this is what's causing the handling issue. Now I just gotta wait til the kit is back in stock.

Do I need a re-alignment after installing the kit?

i think you need to have them add more caster, also your toe looks like it pulls to the right.

i don't believe so but riceandpho suggests you may need to do it again