I want my 4runner to be more pleasant on long trips. Right now it squeaks and rattles, and I have a ton of engine noise. So quieting the interior is a priority.

The first large source of noise is from the engine. Maybe it has to do with me not having the foam damper on the underside of the hood, or the crack in my exhaust manifold, or the fact that I haven't had a head unit for 3 months and I can see the firewall, but the little 4 cylinder is very audible present whenever I'm driving.

Where are good spots to place sound deadening material to eliminate the excess engine noise?

My next source of noise comes from the pedals. A few months ago I did the linear spring conversion for my clutch pedal that was squeaking, but now the bracket for the old style spring is coming in contact with my new linear spring and is unironically making it squeak. This contact between spring and clutch spring bracket only happens when the pedal is fully pushed in and I'm certain this is the cause. Is there any way to keep this from happening?

The last source of noise in my interior is from my brake pedal. I've started having an issue where it (the pedal not my actual brakes) squeaks at the very start of its travel. It seems to be getting more common, is there anything that might be causing my brake pedal to squeak?

For the general interior... it's a lot of work and more money, but pulling every interior trim piece down to bare metal, installing MLV (dynamat type product) on each panel (do your homework, doesn't need to be wall-to-wall, every inch covered) AND installing a layer of noise/heat insulation (luxury liner, overkill or I went with 3m thinsulate as I wanted something unaffected by moisture for my camping rig). It's a lot of work, but the end result is awesome. I'd like to note that the Windows are the source of my loudest sound now (cargo van, not 4r ~ but it was an echoy metal box). When I upgraded my camping rig and went form full windows to no windows, the noise levels dropped aton... so perhaps covering some of the windows would help.. or do like most vans do and have a partition behind the front seats so the noise from 'back there' doesn't intrude.

For the clutch pedal, you'll have to look closely as what exactly is happening. If it's interference then you'll need to address that in a suitable way. Perhaps it's just a slight bend to one of the mounting points, perhaps the spring is too long. Maybe it's hitting on something Else or the pivot point needs a bit of lube?

The brake sorta sounds like it's in need of a master cylinder rebuild. Either the seals are getting old/hard and causing a squeak, or the spring... but could be simply the pivot point needs a bit of lube or something else touching/rubbing.

Both pedal issues need eyes on them to address (and likely ears to help pinpoint the source). But, at least it's not a Safety issue... just an annoyance. It can wait till you get a second set of eyes and ears to help... so make friends with a member here (or anyone into cars who's turned a wrench before) and just start trying things.

Oh man, that’s one hell of a project. That’s Assuming you don’t wreck a bunch of plastic in the process.

I agree with the above on the window glass is a big source of noise.

I would seal up your firewall first. Then look at gaskets for the doors and windows. Obviously fix the exhaust leak and add a hood mat, those are huge for soaking up noise. Get a set of quiet tires.

From there though, the juice isn’t going to be worth the squeeze. Reality is that your old but super awesome 3rd gen 4runner is never going to be in the same class of NVH as the newer vehicles. There’s just too much NVH prevention baked in to them now from the start.

Enjoy that 4runner for what it is. Don’t try to make it something it’s not. Unless your a just have to build a new set of legos kind of person. Then go for it, but you’ll be bored as soon as it’s done anyway….. ( I know several that suffer from builder-itis
, there is no cure.)

Addressing your exhaust leak will help significantly. With sound deadening the more effort you put in the better your returns will be. If engine noise is your primary concern then the BEST way to address that is to pull the dash and insulate the interior side of the firewall with peel n stick sound deadening. That's the best way which requires the most effort. Any amount of sound deadening material you use will be helpful. Here's a few sound deadening write-ups that might be helpful:
3rd Gen 4Runner: Sound Deadening Tutroial & Body Panel Removal
Sound Deadening Write-up
Sound Deadening Project (picture heavy)

I found the source of my clutch pedal squeak. After removing the spring entirely and pressing it in I determined its not the spring, but the alignment of the pedal. The stem of the pedal is off set enough that it is rubbing on the bracket that connects it to the firewall.

I have to adjust the pedal a little over to the left so that it is not rubbing the bracket. I tried taking photos but the odd position and poor lighting makes it look like I'm using a camcorder.

Fix the exhaust leak. Those are stupid loud.

Replacing the door seal on the driver's side door actually made a huge difference. I've done a sound deadening regiment on my 4Runner, you can read about it here: Thinking About Upgrading Your Sound System? Do It! - Toyota 4Runner Forum - Largest 4Runner Forum.

The worst offender in our interior is actually the rear cargo area, it's very, very loud and it brings in a lot of tire and road noise. If you want to start somewhere, start there with a sound deadening material then full coverage of foam. I did two layers of each, as the first layer wasn't enough. After that my cabin go a whole lot quieter. After doing the doors and other spots (I did not do the firewall but did do around the pedals) the nosiest part of the vehicle is now the windows which can't be helped.

ok....im gonna go" against the grain" here.
maybe fix the reasons you have squeeks rattles and exhaust noise first. those noises mean something is loose or worn and like you said a cracked manifold.
things only make noise if something is worn out. maybe just ear plugs or crank up the stereo, but my thoughts fix the problems first