3rd Gen Clunking Solution?

I have the same issue on my 16 auto trd sport long bed. Dealer said it’s due to being a long bed. Did it from day 1. It doesn’t do it when I have it in 1st gear and try to recreate. But when in auto it does it.

 

people saying it's axle wrap..I don't understand how a clunk downshifting from 2nd to 1st, only when cold, would be from that? To me that's a transmission issue

 

I usually cruise to red lights, soon as I let off the gas it starts slowing down and down shifting. Usually about 15-20 mpg 2nd gear when I start to gradually apply the brake and bam clunk when it drops from 2nd to 1st. It also clunks when I put it into reverse from park.
https://m.youtube.com/watch?v=tkuVHIzQXt0

 

I had the same clunking sound, mainly when coasting to a stop or at idle in my 1998 4Runner (same chassis as a 1998 Tacoma/Pre-Runner). It didn't do it when I first bought it from a Used Toyota dealer 8 years ago, but it started after driving it for one year, about 10,000 miles. I let it persist for years after someone on a forum said it was noting to worry about. When my passengers noted it I always told them it was just how it was. I drove it like that for 7 years. I finally got annoyed by it and it seemed to be getting louder and harsher sounding.

I went to a garage with a lift (Auto Skills - MWR on the base) and put some grease into the drive shaft slip yoke and U-Joint as described in the Tacoma/4Runner/T-100 Haynes book. That solved the problem. After a year it starting coming back, so I had the driveshaft lubed again. This time I had Firestone do it and it only cost me $12.00, took all of 15 minutes. No more clunk. So if you do it once year as your Toyota Scheduled Maintenance suggests, you may find it solves the age-old problem. Note: Do NOT go to a stealership. Toyota quoted me 1.5 labor hours for $155 to lube the chassis. Maybe with some smoke breaks and a nap it would take that long. I did it myself in an hour, counting aligning the lift, bay cleanup, et.al Firestone did it in 15 minutes and I watched as they did it correctly. They even put the grease on the steering knuckle contact points and lubed my Moog stabilizer end links (which had grease fittings) as I requested. It's worth the $15 give or take a couple bucks. I hope this solves the problem for some of you like it did for me. I attached a cheat sheet for quick reference.

REF: Tacoma (1995 thru 2004) Haynes Repair Manual, pg. 1-21
REF: 1998 4Runner Owners Manual, pg. 288
REF: Toyota Scheduled Maintenance, pg. 33