My brakes make a squealing noise which is not too loud. there is also a pop sound whenever I come to a full stop

A "Squaling" sound? Do you mean Squealing? Squealing from a stop to moving suggests an issue with the brakes. More information please.
When were the brakes last serviced? Some brake pads are fitted with a layer that causes a squealing noise when they are at their lowest safe thickness.
Is it one long, continuous noise or a short repeating sound. A long noise could be a sticky or seized brake calliper and a repeating noise could be a warped brake rotor.
Do you get any other noises? Such as when your braking or releasing the Park/Emergency brake?
Does it do it when the vehicle is cold like first thing in the morning or after you have driven it for a while? Cold could be a fluid issue and a warm could be something metal rubbing after it's warmed up and the metal has expanded.
Use the comment button below and I'll see if I can help you more.

Most new cars come with ceramic disc brake pads to reduce noise. Aftermarket brake pads, depending upon materials in them, can be prone to squealing. Some pads come with adhesive shims that are designed to absorb vibration and reduce or stop squeal. There is also a compound you can but to put on the back of the pads to do the same thing when you install. Sometimes the noise will go away once the pads have had a chance to settle in .Some are just ornery and won't shut up.

As I look at your letter, which is very good, I might add, here are the few things that occurred to me.
The "loud squealing" should be a belt.
You have one or several belts, and if they get loose, or are worn out ( that includes the belt rubber getting old and hard) they will squeal like that.
However, the squealing also may be coming from one of the pulleys the drive belt or belts are attempting to turn.
If you have a bad bearing in one of the pulleys, you can get that loud sound like " a train".
If you are really careful, a "mechanic's stethoscope" might help you.
That is to take a really long screwdriver, and put the tip on each of the pumps or base of each pulley, and the handle end to your ear, and you can hear the bad bearing "scream" with the engine running.
Be blessed.

inferior pads or improperly installed. it could be that they just need to conform to the disc and the sound will go away, but you should find out that everything else is ok. if you got one of those brake jobs with a lifetime warranty, then its definitely because of the pad material.

sounds like a brake part has come loose.. maybe the self adjuster or the emergency brake cable wire.. it should be obvious when the drum is off

it sounds like it is in the pads and rotors they might be in servicable condition but if they have ever gotten hot they can start making noises and make stopping a little bit harder.

sounds like shims on brakes, or lack of them
thin bits of metal to stop squeel

It sounds like the power steering belt is too loose, tighten it up a bit but not too much just enough to make slipping belt stop.

Sounds like one of the auxillary belts slipping it may just need tightening up. I think the 4-Runner has two belts one large and one for the steering pump

Sure sounds like you need new brake pads. On the brake pad is a small metal tab that contacts the rotor and squeals when the pads need to be changed. Hope this helps. Please keep me posted. Good luck