I wanted to update this thread for future searchers. My multiple misfire issue was caused by a bad alternator and battery.
I ended up replacing the following parts:
1. MAF sensor
2. Spark plugs and wires
3. PCV valve and hose
4. Throttle body
5. Thin vacuum hose on top of the plenum
6. Fuel injectors (cleaned, calibrated, and tested)
7. Fuel pressure regulator
8. Fuel filter
9. Fuel pump and strainer
10. Fuel tank gasket
11. Alternator
12. Duralast Gold Battery
13. Battery connector and 10 gauge frame grounding wire
After replacing items 1-10 listed above, I was still having the misfire issue (P0300, P0301, P0302, P0303, P0304, P0305, P0306) and the engine was rumbling at low idle.
Items 1-5 were pretty standard (I had to get a replacement TB due to my own mistake). Items 6-10 were listed in the FSM. No where does it list alternator as a potential cause of the problem.
After replacing all of the fuel components listed above (items 6-10), it began to run stronger. At low idle (600-700RPM range) it was still sputtering, but the engine was no longer dying. So I am glad that I did replace those parts because the fuel injectors were not properly operating before cleaning and the fuel filter did not look very good either. The fuel strainer was also pretty brown after 16 years.
I thought to try the alternator after I finally found this thread:
http://www.toyota-4runner.org/3rd-gen-t4rs/237920-misfire-mystery-3.html
I bought a Harbor Freight multimeter and watched a couple of YouTube videos to figure out how to test for a failing alternator and battery. The fluctuating voltage (around 12.6 volts) while the car was running showed me it was a bad alternator. I also realized that my dimming headlights and other electronic components were a symptom of a failing alternator, and I had been ignoring that issue for a while.
When I finally looked at the alternator, I realized my next problem. The shop that I went to last year to replace all three belts forgot to replace the long screw, bolt, and nut that hold the bottom of the alternator in place and tension the alternator belt. The long top screw on the alternator and the pressure from the bottom alternator bracket were the only things holding the alternator in place and running that belt for over a year.
I bought a Duralast remanufactured alternator from Autozone and ordered the specialty screw, bolt, and nut from the dealer. The part numbers for those parts are:
16385-62020 - slider, fan belt adj
90119-08493 - bolt, w/wa
90179-08183 - nut
After replacing the alternator (don't forget to put some dielectric grease on the back connector), I used the screw, bolt, and nut to properly tension the alternator and alternator belt.
I then cleaned my leads and negative battery connector with a wire brush and some sandpaper and I replaced my positive battery connector with a new Duralast Gold zinc battery attachment.
After reading up on potential grounding issues, I realized that someone had long ago cut the frame grounding wire near the battery. So I cut some 10 gauge wire and crimped on some #10 leads and replaced that wire as well, which goes from the frame to the negative battery terminal.
I started her up and she has been running stronger than ever. I probably didn't need the fuel pressure regulator or the new fuel pump, but I am glad I did all that work. The fuel system is in top notch shape now!