Caliper upgrade???

Ah, there ya go LOL. Yes, that is the way it is with old braking systems. Sounds like you are getting there. BTW, if you have not replaced the rubber lines, do so ASAP. Did you replace the rear wheel cylinders? Do so; they are cheap.

Being where you are at with the dryness, the hard lines may be just fine.

Did you bench bleed the new master cylinder? If not, then there is likely air trapped still in the MC that will absolutely effect the braking.

As for the 'thunk', well, it is pretty hard to hear and feel it from this side of cyberspace, but I would be more inclined to expect a worn suspension bushing or ball joint.

For the wheel bearing, both inner and outer consist of a bearing cage assembly and a race. The races are an interference fit into the hub. Once you pull the hub the outer cage falls out, and then you remove the inner grease seal and the inner cage falls out. The races may look like part of the hub, but if you clean out all the grease, you will look through the hub and see some slots in the hub casting on the far side with a metal ring visible through the slots; this ring is the back side of the race. You put a tapered punch through the slot to the back of the race, and drive a couple of whacks on one side, and then the other side, than back and forth, and that will slowly drive the race out of the hub. Do this on both sides. Be careful to minimize any nicks in the hub's inner surface, and sand out any that you make. Then you use a narrow chisel with the end flattened and the corners smoothed (so as not to gouge into the hub), or a proper race driving tool, to slowly drive the new races into the hub, going around and around to drive them in evenly. (Sorry if you know all of this already...)

I was not thinking of the PST kits but of other cheaper kits. I'd expect PST to be good, but about the same as NAPA for the rubber parts, ball joints, tie rod ends. And the PST kit does not include the pitman arm; that is the arm that sticks down from the steering box. It has a joint at the steering linkage end that is subject to wearing out. It may have some parts you don't need like anti-sway bar end links if you don't have that on your car.

BTW, for a pure street car, I'd stick with rubber, not poly. Poly does a great job of tightening the front end up, and taking out some variableness, but it will typically beat up frame and suspension parts on a street driven car that gets lots of miles. I always used rubber in the front ends of my rally cars, for that reason; poly would have beat the crap out of everything. (Of course, rallying is a pretty severe application!) So this decision depends on what you will be doing with the car.