1996 Toyota Prado Knock in drive system?

I have a 1996 Toyota Prado, Auto. When I take my foot of the accelerator when cruising say around 60 for example there is a knock in the transmission? Or something, somewhere. Have replaced the front diff (which was full of water when my mechanic removed it) made no difference, have replaced all the front suspension, no difference. My next thought was the transfer case, could this be it, after this I guess gearbox? No one can pinpoint it and I'm out of cash after the last repair. When I tow my trailer and reverse if the car becomes under strain, say. Going over a kerb or something, I get a loud screech coming from somewhere, gear box, diff, I don't know, I think this may be related? There has also been a few times over the years where I have thrown it into reverse a bit to quick while it was still moving and this produces the same screech noise, this is probably how it all started?

To explain the knock a bit better the other day I noticed towing my trailer (which I believe is partially to blame for the knock) that when I brake and the push brake on the trailer jams on and off it is a very similar feel to the knock in my car with out the trailer but not as heavy a knock as with the trailer on. The knock happens when you take your foot off the accelerator while accelerating, when you put your foot back on the accelerator even just real slightly or hard?

Hope I haven't confused you too much, hard top explain.

Regards
Jason