I went to the stearship and they said I should put in new break pad shims when replacing the pads and they wanted $50. (wow just as much as the pads) Since I never heard anyone mentioning replacing them.
DO I NEED TO?
are the old one good enough to leave on?
Do they prevent brake noise?
the non-OEM shims are about $10 at a parts place.(I think that makes it $20 total)

any suggestions from others that replaced their own breaks

FYI 03 4R Sport (17")

Oh they sold me Toyota pads #04465-35290 for $61 (I assume they are ceramics)

Also are there any parts I need to grease while the front wheels are off? example: wheel bearings.

Many aftermarket break suppliers integrate the shim into the pad. Wagner thermo quite is known for this. I wouldn't pay $50 for shims. Thats the same price as the pads.

Typical stealership response.
I replaced mine because they were damaged (due to the frozen lower inner piston; search for the write-up somewhere here.) Don't replace if they are undamaged. Just clean and relube with brake grease.

I read so much on this forum that I should stick to toyota pads but I have heard Wagner thermo quiet are being used. How have other's experiences with them?

I agree! The shim kits are vital in maintaining your oem braking operation. Toyota has been using shim kits and anti-squeal kits for decades on their brakes. I ran into this with my old 95' LS400. I tried aftermarket pads, only to find noises (groans and squeaks), and clicks due to the pads shifting in thier caliper seats. I tried aftermarket rotors too... At the end of the day, and about $1,500 later in parts, I was back to genuine oem all around, and was happy.

When you take your old pads out of the caliper seats, you'll see the shim clips over the back, with an insulator pad between the clip and pad. Just clean them up, sandwhich a little grease on the insulator pad, put the clips back on and reuse them on your new pads.

One suggestion: By a few cans of brake cleaner, and have a few old towels handy to lay on the ground under the brakes, and have an old toothbrush. Spray the seats in the calipers with the cleaner, use the toothbrush to clean them, then rinse with a fresh dose of cleaner. It's a messy job, but one you'll be happy you did.

I bought the shim kit from Partznet pn# 0494535120 for $ 34. Mine were not in good shape. It is hard to tell if you need them without removing them and inspecting them.

There is a TSB out about loss of solid brake feel or something on 4Runners so Toyota redesigned the shim kit which now, instead of one shim per brake pad, there are two. This apparently takes care of the brake issues some people are experiencing.