Engine started running rough

That does not sound good. Is that noise coming from the front of the engine or do you have the exhaust modified?

When it bogs down does it stall? Can you do a video of the problem when it stalls or?

Okay, reading through this it gets a bit murky. In one post you say it runs okay until you put it in gear and another where you say it runs bad until you put it in gear.

You say you cut off the converters, what did you do with the 02 sensors?
It sounds like it is missing, what does the spark look like at each plug? You replaced a bunch of parts, was that before or after it started this?

Okay, so it was running fine, you shut it off, came back out and it then started skipping and lost power if you tried to give it any throttle. In response you installed a new timing chain, then O2 sensors, cam sensors, TPS, and removed the converters. After all those it still runs the same with missing and low power, but seems to idle fine.

Was there anything else like plugs, wires, coils? You say it only acts up when shifted into gear? Will it also drop out if you just put it in park or neutral and stomp the gas?
The video did not sound real good but it sounded like a lot of exhaust leakage was masking the rest.

What do you have for test gear?

I am asking all this just to get the problem clear in my head. I would be the last person to tell you to swap it unless it was something that the repair would cost more than a replacement engine.

Okay, that sort of rules out that it is a wiring harness that is being moved around when you shift it into gear. What does it do if you manually shift it into low/second/drive? Does it still bog down and lose power?

I am thinking that it is possible the issue is not the engine but possibly an odd transmission problem. If the overdrive clutch were to lock on it would act the same way when you put it in gear because the converter would not be able to actually work.

The thing is that it does not seem to act up until you put it into gear. Then you say it bogs down and has no power. That sounds a lot like the torque converter is damaged or locked up. Used to be a common issue on some GM cars. The converter clutch would lock on and while you could drive the car it would bog down and stall because the converter could not freewheel.

If it is not recognizing the key you may want to try another key. It could be a key failure only. Or it could be related to the earlier issue and be a faulty PCM. That would require a factory level scan tool to test the PCM itself.

1998 and up use a PATS key. Inside the key is a chip (not really a chip but the same type of item used in store theft tags) this is programmed into the trucks anti-theft system and the system reads the key every time you try to start the engine. If there is a fault in the key, the anti-theft or the PCM the engine is not going to start. The first step is to try a different good key. However, having only one key means you cannot program any extras yourself as you need two known good keys to program extras without a scan tool or locksmith key programming tool. As this was a sudden failure it could very well be that the same issue that was causing the poor running has now failed completely. However, without a working key there is not any good ways left to test and you now need a high end scan tool that can actually talk to the modules directly to see which ones are working or not.

When you try to start it what does the security light do?