No charge error light?
Battery connector and post clean all the way to bare metal? Gun-metal/gray is not bare metal in electrical terms. Bare metal is silver or copper, depending on connector material.
With engine running
Measure voltage at battery post - yes the lead post itself.
Measure voltage at alternator "B" post. There should be very little difference if any
...should i be looking for a loose wire or something small like that...
Absolutely.
or do I have a larger overall problem with the electrical system of the car...
Hope not. Hoping it's just a loose wire/poor connection somewhere.
Something could be wrong with the wiring. Sometimes, people suspect the alternator and replace it, without
verifying that it's really what's causing the problem. With new alternator, system still does not work (of course). Then people say that that re-manufactured alternator is also bad. A brand-new premium alternator with gold wire for windings and titanium housing would not fix the problem, because the really defective part of the system (the wires) are still there.
Do a thorough check/voltage checks of the charging system first. IT will not cost you a dime, and may even save you from buying another alternator that will not solve the problem, after all.
This 22RE charging system should be close to your truck's.
Also, if your system has this...Also Open and inspect it.
This looks like a ferrite choke but it is not.
(We're not choking ferrets -Who's line was that BTW? LOL!)
This is the equivalent of the appendix in human terms. I am not aware of any 4Runner owner on T4R.org or Yotatech who had put this to any use in the past 30 years.
If there is poor connection here, your regulator will see good output from alternator, so you will not get the "Charge" error light. So you would think your charging system is working properly. However, the truth is that alternator output is never reaching your battery.
Take it apart, clean everything thoroughly down to shiny bare metal, re-assemble. Better yet, replace the whole battery to alternator wire with one continuous piece of thicker brand-new wire, and scrap this useless part.