97 Eddie Bauer 4WD- many problems - Please help!

I apologize for the long post. Bear with me...I bought this thing in January. Since then, I've dropped $400 on the A/C and roughly $700 to get the check engine light off. It goes off for a while, only to come back on, for no rhyme or reason. It is now an intermittent problem, coming on a few days a week. Have had the codes checked several times. It comes out with a list like a mile long.
Also, idles very rough sometimes. My mechanic gave me a technical service bulletin re. a "booming noise heard at idle" due to a faulty exhaust system, but neither the dealer nor the muffler shop I've talked to can get the parts to fix it. I was told that it would be roughly $1000 if I could find the parts. Is a custom exhaust a feasible alternative?
Next - The brakes squeak really bad at low speeds. I was told this was because they didn't turn the rotors when they replaced the pads.... Now it has developed a new squeak - more of a squeal really...like nails on a chalkboard, when I drive at low speeds. This seems to stop when I let off the gas, reach approx. 25mph, or step on the brake, only to be replaced by the other loud squeak.
It also started making a loud clicking noise from behind the radio. It makes it regardless of whether the A/C is on or not. It eventually goes off, but comes back if I turn the A/C on. Coincidentally, my A/C can no longer decide whether to blow hot or cold. It goes back and forth.
One more thing, I know it's a big car with a V6, but I'm lucky to get 13mpg in the city. Does that seem right? Could it be related to the exhaust problem? Any ideas on how to improve it?
Thanks for taking the time to read this! Please help!

I got a 96 EB and I get 12 miles in the city. It's just the big engine.

I cleaned the mass air flow sensor on my truck, and it is like a new truck. The difficult part is getting past the tamper screws. I was able to remove the one in front with pliars and the rear one I drilled out the center tab and then used the star head. If you do this yourself make sure you put a silicone gasket on before install, the factory didn't do this. Now I need some 4x4 help. Hubs

Okay as far as the check engine light goes we found it was the gas we were using. There must be a sensor of some sort, probably in the smog setup (we're in CA). Once we upped the octane to 91 we were fine.

On the squealing noise - I really do know what that is! It took us forever to figure it out though. For us it was the dust shield(s) on the wheel ends. We have a 1998 Eddie Bauer, so that shield has gotten hard and has been rubbing on something causing the squeal. We can only temporarily get rid of it by greasing/lubing the shield.

Hope that helps,

You can try a KN fuel injection performance kit or a cold air intake kit that will help on the gas mileage a little not much though and it will also help on the horse power a bit. the rough idle can be attributed to a poor or a bad working air idle control valve throttle positioning sensor or the real culprit could be a bad EGR valve or EGR valve sensor. hard to tell with out the codes but its strange that you upped the fuel grade in the truck to help out on the check engine light because the most common problem is that the newer vehicles are designed to run the cheap stuff and buy upping the octane you mess up the oxygen sensor that then makes the check engine light come on. I don't know why. But as far as the squeaky brakes try some caliper lube or squeak be gone you can pick up the small packs of the lube at any advance auto for like a buck. As far as the other squeak it could be in the rims if you have aluminum rims on the truck. My 99 does this from time to time I found that on mine if the rims are not torqued to the specification or over spec. the rims will make a squeak. Don’t know why either. The clicking noise behind the radio sounds like a relay or something.

I apologize for the long post. Bear with me...I bought this thing in January. Since then, I've dropped $400 on the A/C and roughly $700 to get the check engine light off. It goes off for a while, only to come back on, for no rhyme or reason. It is now an intermittent problem, coming on a few days a week. Have had the codes checked several times. It comes out with a list like a mile long.
Also, idles very rough sometimes. My mechanic gave me a technical service bulletin re. a "booming noise heard at idle" due to a faulty exhaust system, but neither the dealer nor the muffler shop I've talked to can get the parts to fix it. I was told that it would be roughly $1000 if I could find the parts. Is a custom exhaust a feasible alternative?
Next - The brakes squeak really bad at low speeds. I was told this was because they didn't turn the rotors when they replaced the pads.... Now it has developed a new squeak - more of a squeal really...like nails on a chalkboard, when I drive at low speeds. This seems to stop when I let off the gas, reach approx. 25mph, or step on the brake, only to be replaced by the other loud squeak.
It also started making a loud clicking noise from behind the radio. It makes it regardless of whether the A/C is on or not. It eventually goes off, but comes back if I turn the A/C on. Coincidentally, my A/C can no longer decide whether to blow hot or cold. It goes back and forth.
One more thing, I know it's a big car with a V6, but I'm lucky to get 13mpg in the city. Does that seem right? Could it be related to the exhaust problem? Any ideas on how to improve it?
Thanks for taking the time to read this! Please help!
Ok, i might be able to help you with at least one of your problems. It is coincidental that your explorer makes the noise behind the radio while you are having climate control issues, i have seen quite a few of the blend doors split(right where the actuator slides in) on explorers, it also makes a popping noise dealing with the same concern b/c the actuator(the electronic servo that switches from hot to cold) is turning while the blend door is not. this can be a costly and difficult repair. If you happen to know the codes for your check engine light, i may be able to help you there too.