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So neither of these are likely to be pinging since the flight crew was probably incapacitated and the pilot or copilot would have turned of the main transmitter.

At what point were the pilots incapacitated and what was the cause? I cannot buy the fire explanation because they stayed aloft way too long.

This scenario seems to indicate a third party being the instigator, doesn't it? flat out hijacking. But, there is supposed to be a quick way to add that info to the transponder squawk. Isn't there?

>>At what point were the pilots incapacitated and what was the cause? <<

I said the flight crew was probably incapacitated, not the pilot(s).

I still think it will come down to the senior pilot losing it and going rogue due to political events in Malaysia the day before he took off.

But, there is supposed to be a quick way to add that info to the transponder squawk. Isn't there?

A transponder uses a four digit code. Squawking that code is the description of having the transponder turned on, and tuned to the correct 4 digit code. Yes, that takes but seconds to accomplish.

The airplane flying to standard waypoints indicates the flight plan was input to the flight computer. That takes a minute or three. Two guys in the front office of that airplane are trained and skilled in programming the flight computer. They become the prime suspects. The erratic altitude,however, indicates someone less skilled in manipulating the autopilot. OR, someone who wanted to make it LOOK like a hijacking. I'm still looking at the pilot in command, as he had the flight simulator to practice routes, fuel consumption, etc. He's by default the likeliest to have done this.