I'm trying to figure out why my front windows don't work.

Both rear windows work from driver control switch.

It happened after removing the security system. In that process, I removed 6 T-tap connections (but left the taps in place). I'm thinking I maybe pulled too hard on one?

So, I'm looking at the Diagnostics section of the FSM (for 2002) There are 9 sections:

1) Engine (DI-1-156) (FSM p177)
2) AT (DI-157-220)
3) ABS w/ EBD & BA & TRAC & VSC (DI-221-374)
4) SRS (DI-375-468)
5) Cruise Control (DI-469-488)
6) Engine Immobiliser (DI-489-510)
7) Body Control System (DI-511-550)
8) Back Door Control System (DI-551-575)
9) Air Conditioning (DI-576)

The logical section is the Body Control System, yet I don't find the front window circuits described there. It must be there, but I am not seeing it. Can anybody help me out, if you have that (or similar) FSM please?

It's not in the FSM. You need the 2002 Toyota 4Runner Electrical Wiring Diagram Manual. I just did a google search and saw one on ebay for $45. Very handy to have. Here's a Dropbox link to a 2000 4Runner Wiring Diagram Manual which might be close enough.

2000 Toyota 4Runner Wiring Diagram
Dropbox - 2000 4Runner Electrical Wiring Diagram (EWD383U) - Printable - Simplify your life

@Deej101 FSM RM887U - Body Electrical - Power Window Control System - BE-60 thru BE-71.

Funny, was just looking there before I saw your post. So, from page BE-7, the flow for checking if *one* window does not work is:

1. Power window master switch
2. Power window switch
3. Power window motor
4. Wire harness

Since it is *two* windows, I think I can eliminate 1-3, right? Because it is unlikely for those to fail in 2 doors simultaneously. Which leaves me at wire harness. The question, though, is where exactly. Time for me to get comfortable with using a multimeter to probe things....

Your FSM a working PDF search "window" in search bar, scroll results harness and connection points.
Get comfortable, may have to get what I call getting "intimate" using FSM VOM and Harness.

Have hard copy EWD425U you hit wall.

Well that sent me down a bit of a rabbit hole, lol. But making a note of who has the holy grail (2001 wiring). Don't be surprised when you start getting DMs from me. For reference sake, here's what I know so far:

EWD383U (2000)
EWD425U (2001)
EWD471U (2002)
EWD514U (2003)

I have the full 2002 FSM, including 471U, which is my main reference material. I have misc pages from some others. One day I hope to own a paper copy of 2001.

Is there a current page here on site compiling resources? Seems everytime I've looked, many links were outdated/broken.

Anyway, back on track: after taking apart the door again (also did passenger door this time, cleaned up door lock actuator and switches) and putting it back together, now the windows work again, BUT now the driver side wont stay up. It hits the top and acts like theres an obstruction and comes back halfway down. It was late last night so just managed to get it mostly up for the night. More troubleshooting ahead.

Btw, this will sound lame, but when, in the course of doing electrical diagnostics, it says to "connect battery +/- to pin X" umm, how physically do I do that? Remember, I'm an elec noob. My first instinct is I need to connect a wire to the car battery and run it into the cabin where I'm working, but I know that's not right. More likely I need to find a wire under the dash that already does thst. What is common practice?

Anyway, thanks for your help!

I think that the Power Windows section of the wiring diagram manual would be of huge help. Hopefully someone can post a link to the 2002 manual.

Power Windows
Dropbox - 2000 4Runner Electrical Wiring Diagram (EWD383U) - Printable - Simplify your life

Yes, I do have the full 2002 manual, including electrical. I'm still learning how to read the wiring diagrams. Getting there, slowly.

Thanks for posting that link. I was more looking for a troubleshooting flowchart, like they use in the Diagnostics section, though. I think I found the closest thing they have on BE-7, which just narrows it down to the wire harness.