Okay..
I have had the truck back for a week now. I think it is safe to put my story up.

As you all know, I lost compression in a cylinder on my truck early January.
I had done a leak down test (first time for me) and it showed a bottom end problem, as the cyl lost pressure into the crankcase.
I did a lot of reasearch and a lot of shopping around.

I knew the problem was in the bottom end of the motor.

I found that a crate motor from Toyota is upwards of 10 grand (ouch).

I started calling junkyards. I found one listing a 1GR in Miami in a rollover Tacoma for $900.00. I asked Miguel (XtoplineX) to go check it out for me (Thanks Miguel!). He did, and we found out it was a mistake, and it was a 4 cyl.
Back to the drawing board...
Another junkyard (happens to be local) found one in North Carolina for $2600.00 - it had 7,000 miles on it.
This was the route I was going to go. The plan was to buy the spare motor, drop it in my truck, then I would have my old one that I could build for racing.

In the back of my head.... I wanted to take it to Toyota for them to check it all out... I figured.... If I was going to take it to a stealership, I am going to put it all back to stock, reset the computer, and play dumb.
So I did.

I drove it to Toyota (on 4.5 cyls LOL). I parked in the service driveway and a writer came over to me. I explained my problem (major loss of power, bad idle) He then got in my truck and revved it up. He said it sounded fine. I told him there was a problem.
He then called a "Master Tech" over to us, and asked him to drive it.
I went with him.
The guy bearly gave it any gas at all. I told him he had to get on it for the problem to bear its ugly head, but he would not. He then told me that if there was a problem, the CEL would be on. I told him that I had previously uninstalled my train horns, so my battery was disconnected. It would have reset the codes.
We got back to the dealership, and he walked up to the service writer as I waitied in the truck.
The service writer came up to me and said there was nothing wrong with the truck, and I must be imagineing it.
I told him there was a problem , and I was not leaving until they acknowledged it.
Another "Master Tech" came out to my truck with a scan tool to look at my computer. he said there are no codes, so nothing is wrong with the truck.
I told him there WAS a problem. He then found the "Pending" codes in my computer (P0420 + P0430). He told me they were there. I explained to him that I knew there was a TSB on these trucks about that. They would not do anything about it, because I had a Flowmaster muffler on my truck. they say that the Flowmaster caused the cats to blow out, even though there is a TSB about faulty cats in these trucks.

Side note - I actually gutted out my cats after the supercharger had its way with one of them anyhow

So... The service writer comes back up to me. At this point he has a REAL bad attitude with me, and is yelling at me in the middle of the service department, with customers looking on. I loked at him and said very politely "Do not yell at me one more time". He then brought his tone down to a reasonable level. He said he would have my truck checked out by the service manager in the morning.

So... He tells me to leave the truck and they will diag it.
I do.

I get a call the next day from the service manager.
He says the "loss of power" I am feeling is due to the free flow exhaust with the Flowmaster muffler.
I told him it was not.
We argue over the phone for about 45 minutes.
FINALLY I am done playing games, so I tell him to run a compression check.
He tells me he is not going to spend the labor time on a problem that does not exist.
I told him I wanted it done.
He told me he would not do it unless I paid for it.
I made a deal with him.
I will pay $85.00 labor for the compression test if they find nothing wrong with the truck.
If they find a problem, I do not pay.
He agreed.
I never got a call back.
I finally called them back 2 days later
The service manager says - and I quote "Mr Bastos, you really do know your stuff".
I ask why?
He said there is low compression in one cyl.
I then ask what the deal is with it, he says he will have to get back to me.
So... another day goes by, and he says the head gasket is shot. I ask him how he knows this, and he said they tore the head off and have determined its the head gasket. He asked if the motor overheated. I said no.
He asked how this could possibly happen, I played dumb.
He said he will contact me at a later time with more info.

The next call I got was from the service manager again.
the conversation goes like this:
Me "Hello?"
SM "Rob Bastos please"
Me "This is him"
SM "Hi Rob, this is XXXX from Toyota. Are you aware your truck is all over the internet with a supercharger installed, and you driving it? It is even on the manufacturers web site who designed the supercharger."
now a slight pause....
Me "How much to fix my truck?"
SM "You need a head gasket. You shouldn't have lied to us, we would have found it earlier"
Me "Look.. You guys should be able to diagnose a problem regardless of the cause. Its an engine. The problem was so elementary, and I had to tell you what to look for."

At this point that damn SM is yelling at me again. I hung up on him.

I call the dealership and ask for the general manager of the dealership. I am told no one is in, but they will be in the following morning, and the only person available was a sales manager.
He got on the phone, and I told him I was mistreated, and the SOB SM kept yelling at me.
I told him the next step would be me coming to get my truck in about a half hour. I will bring it to another dealership to do the repair.
The sales manager tells me okay, no problem, and thanks me.

About 15 mins later I get a call from the Service DIRECTOR from his home.
I tell him the whole convoluted story, and he makes a deal with me.
He said Rob, you pay $2,050.00 for the head gasketS to be replaced. If we find any additional problems with your truck, we will cover it under warranty. He chose to do this because of the treatment I received in his shop.
I told him to go ahead.

SO

couple days go by..

they replace the head gaskets

And guess what??

NO DIFFERENCE.

Then I get a call telling me they are tearing apart the bottom end of my motor.

I go up to take pictures when they found the broken pistons and crack in the block.

Anyhow....

the dealership put a motor in my truck.
I paid $2050.00.

I picked up my truck, and they stole my damn Radar detector.....

The dealership told me they would reimburse me for the replacement.