There's really nothing special about installing a lift with KDSS. Any competent shop should have no problem working with it.

A few tips:

The lift height has no influence on tire fitment unless you're changing the mounting points on the IFS (bracket lift) or going to a long travel suspension.

The lower lift heights will drive better. The high angle front lower control arm position of taller lifts inherently transfers more bump into the chassis. There is nothing any shock setup can do about that. But the shock choice does matter a lot for ride quality. You will also have more useful suspension travel and articulation keeping the lift height relatively moderate. I think around 1-2 inches is ideal balance. YMMV.

KDSS solves the body roll issues generally. So I would not recommend matching KDSS with digressive valved shocks. It gets pretty harsh at that point. I would look for linear or progressive shock valving, and I would tend to look on the softer side. IMO the Fox 2.0 snap rings or ICON snap rings would be a great choice as a moderately priced lift option. ICON IIRC are digressive in rebound only, but nearly linear in compression and are pretty soft. Ride quality is excellent. And price is great too for what you get. There are other good options as well. Just depends on budget and needs. The best thing you could do is actually drive a few with different shock setups to see what you like.

I had Fox 2.5 Factory Race RR on mine. They worked well. If I were buying again - I would buy from Accutune or another similar shop and have them valved softer. I have the Fox 2.0 on my Tundra - it's not an offroad truck, just a daily driver and tow vehicle. The valving is excellent on them. Significantly nicer to daily drive than the 2.5s.

There are a lot of different lifts sold by toytec, so $3400 is either way overpriced or fairly priced depending on what setup they are installing.

If you lift over about 2 inches you'll want new upper control arms that fix the caster issue. The suspension loses caster angle as you lift it. It's due to the effect of the uneven A arm radius arcs and the axis of the two arms. The lower control arm adjustments run out of adjustment room and the most common "fix" is upper arms that have slightly different geometry. If you don't want a lot of maintenance - look for upper control arms with ball joints not spherical bearings (also called uniballs). Ive tested a variety of options.

I recommend looking for upper control arms with rubber OEM style bushings and ball joints that are not proprietary. There are a variety of reasons, but rubber has the benefit in this application due to the softer material reducing peak loading on the ball joint and the spindle and has plenty of range of flex for the travel of the front suspension.

You do not want Tuff Country upper control arms. If those are offered - ask for something else. They do not correct the geometry properly. Tuff Country Ball Joint UCA Review (Updated w/ specs vs JBA and OEM)

KDSS will always tend to lean some. It's inherent in the nature of the hydraulic system that is unbalanced. The pistons will always have a net force extending them via the accumulator gas pressure acting on the cylinders and the net force area differential of the piston shaft. So it will always push down on the driver's side and would need to be offset by shims or springs on the passenger side or accept a slight lean.

Plan on an alignment when it's done. If the shop isn't including that - make sure you have somewhere do it. Due to the age of your 4Runner, plan on having to replace all of the lower control arm adjustment bolts (cam bolts) and associated hardware. In most cases they will end up needing to be cut out to be removed and replaced. They almost universally seize within the first few years. Maybe you'll get lucky and they'll free up, but I would plan on that in your budget.

Good luck!