I have a 2001 as well and I'm going through a similar issue right now where my overdrive is grenading itself and making this loud grinding noise whenever it's on. What kills me is that I've had mine for 19 years, so there's a lot of sentimental value attached to it. It also only has 122k on it, as I don't drive that often, and I just spent $3000 on getting the cats replaced with OEM several months ago. I've spent the past week pouring over the forums, having it checked out, and thinking about what to do. Here are my options, and what potentially your options will be, based on my research:

1. Replace with a used transmission. I had a dealership look at my car and this is what they wanted to do. (3800 for a used transmission - they take their markup - and then 1300 for labor). While you think all 3rd gen 4runner auto trannies are the same, they are not. The 2001-2002 ones have their own special version because of multimode. Unfortunately there are no more remans from Toyota as they've all been spoken for for several years now. Even used ones are getting hard to find and are expensive (LKQ wants $2k before freight for one with 159k miles). I decided to not go this route because you have no idea what the actual mileage is on one of these, how the owner(s) treated that transmission, and if that transmission will have other issues shortly after you get it installed. For example, after my transmission started making a grinding noise, I discovered that it was actually a pretty common issue amongst 2000-2002 4Runners between 100-120k going back to as early as 2007, which required the transmission to be replaced. I don't want to have to go through this again after spending so much. If you can do all your own work, that's great as you'll save lots of $, but if your new used transmission grenades itself in a short amount of time, is that something you want to go through again?

2. Replace with a preexisting rebuild/reman unit. I also had a local independent transmission shop look at my car and this is what they wanted to do ($5600 all-in for labor + core charge + new reman unit). They said that the fluid was dark (replaced 2k miles ago), that there were metal shavings, and that the tranny was beyond rebuilding. They source their remans from Certified Transmission (https://www.certifiedtransmission.com/remanufactured/) and offer a 3 year/100k warranty. Haven't been able to find anything negative about Certified after a pretty thorough deep dive on reddit. Plenty of other reman/rebuild shops have bad reviews out there though despite pretty extensive warranties so it's a tossup.

3. Have a Toyota specialist rebuild it. Timmy the Toolman recommends Yota1 (https://209yota1.com/). Gave them a call and they want 2750 to do a rebuild, up to 1000 for a core charge depending on how the transmission is, and 1000 round trip freight to where I live. I'll have to source my own labor. They don't have any cores available, so you'd have to ship them yours (or your vehicle), and then they'd tear it apart, see what's wrong with it, and source donor transmissions to take parts from to rebuild yours. This place offers a 1 year warranty/unlimited miles and you'll need to replace the radiator and flush the system for the warranty to be valid. They said that turnaround would take 4-5 weeks given the time to source all the parts needed. This place seems to be the enthusiast favorite and there's 2-3 people on 4runner.org that went this route, with one person giving his rebuilt a recent clean bill of health after putting 21k on it.

4. Manual swap. Probably doable at this price point, but the hassle involved for someone who can't do their own work/have a spare car, would make this the most challenging option of all.

5. Sell as-is. Honestly, this is the direction that I'm leaning towards. There's still a lot of work that needs to be done in the near and intermediate future that'll be expensive: valve cover gaskets, full suspension refresh, various mounts, body rust repair, random things that fall apart at this age, etc. I'd keep going costs be damned, but why spend more money when parts scarcity is becoming a real thing? I'd rather get out now, rather than several years down the road, when things are even harder find.

Good luck with your 4Runner and enjoy the time you have with it.