Well I went to Toyota since I got a P1135 check engine code (they fixed this, it was the O2 sensor bank 1 sensor 1) and I was hearing a strange sound when accelerating after initially moving (did not happen from a stand still).
The sound seemed like the tranny was having a problem engaging into proper gear after moving, coasting (or maintaining speed) and then reapplying the gas, but I was unsure it was the tranny at the time I spent over $1000 in maintenance at Toyota and asked them to look into this problem. I got the 4-Runner back and the same sound was there. I figured it could not be too bad of a problem until it left me stranded. Now when I put the car into drive apply gas, all I hear is what sounds like nuts and bolts hitting each other where the tranny is!

This is a 2001 w/ 90K miles and we have done all the maintenace at regular intervals and I just got a tranny flush too!

What do you think?

Thanks!

Whoops I meant to ask if anyone thinks Toyota could have made a mistake to cause this failure? I got all my 4x4 fluids changed as well as the tranny flush.

I doubt they made a mistake. Most likely is that the transmission flush caused you problems. You need to get someone to price you repairs on that. In the worst case, you should start hunting for a good used transmission.