Shuts off while driving?

Hello, if you can put your foot on the gas pedal and hold the throttle open a little and it will keep running, then the Idle air control valve is either not opening fully during a cold start up, but still able to open enough after the engine is warmed up to keep it idling. The 2nd issue almost sounds like a thermal/heat related issue. Possibly a solder joint in the PCM getting hot and opening up. The solder joints will close back up when the PCM cools down. There are a couple TSBs, one is water intrusion into the PCM, the other is a connector issue. So, it's possible that if the PCM has any water intrusion and corrosion on the circuit board, you can have issues like this.
Because this is not a drive by wire setup, where you have a throttle cable running all the way to the throttle body and throttle position sensor on the throttle body, the PCM might be losing that TPS signal, if you had a scan tool on the vehicle and watching the PCM live data when the fault occurs, you should look to see if the throttle position sensor voltage is moving with pedal travel.
I'm wondering if all the poking at the connectors has caused a connector pin fitment issue. But Ill post the location of the PCM so you can check the connectors and PCM for any corrosion on the PCM pins or around its case. Is the Check engine light coming on when the throttle issue happens? There should be a code setting for that, if not, it might be a solder joint where the PCM is actually losing power or ground.

The 1st diagram below shows the Idle Air Control Valve and the PCM location on the driver side inner fender, that's definitely a location where water intrusion is possible.
Diagrams 2, 3, 4 are the Throttle position sensor, the fact that you are losing the throttle control sounds like you are also losing fuel injector control. If the engine is staying running during this fault, then there is some idle fuel injection control happening, or all control is being lost, and it's just the vehicle rolling to a stop. But all this should be able to be monitored by watching the PCM's live data. If your scan tool loses communication during the 2nd fault, then you know the PCM is losing power or ground.

Diagrams 5-10 are the TSB on PCM water intrusion, but even with a basic OBD2 scan tool that can only read engine data, this issue should be able to be diagnosed. There has to be a scan tool data PID that would stand out especially during the 2nd fault. But check the PCM connectors for corrosion as well as the PCM case. Make sure the key is Off before disconnecting the PCM connectors. I would also keep an eye out for any wiring sections that some of these shops might have been back probing or messing with connectors.

Did both of these issues start happening at the same time, or did one start first?

If the Check engine light is on, what code is the PCM storing? You mentioned if you keep your foot on the pedal, you can keep it running? If that's the case it sounds like the engine is not getting enough air during cold start up, which would have something to do with the Idle air control valve. But the Pass lock system has 3 components, the key, the sensor in the Ignition switch and the Pass lock module under the dash. I would see what codes are stored in the PCM, even if the check engine light goes off, there will still be a history code stored. Thats just a fault coming and going, or the PCM losing its memory and losing the code due to a power loss.
What components have been changed? Sometimes a fault can cause tunnel vision. But start with any stored codes or lack there of. If the codes are missing, after the check engine light has been on, that tells you the memory of the PCM has an issue. There is a 12volt permanent feed that keeps the PCM memory, if that's lost, so will the codes. That will point to a connection issue. These vans are also known for the engine compartment fuse panels having issues due to their location. I have seen them just moved by hand, and the PCM lost power. And I know these have PCM connector issues. But here is the info on the pass lock system and how it works. It's possible one key is having an issue, on the 3rd diagram below is the live scan tool data that would be expected from the security system and can be used to determine if it's actually the pass lock or something else cutting out. Really the best way is to watch live scan tool data when this fault happens.
It's possible to have multiple issues, or just one connection issue showing as multiple issues, since everything is tied together. The pass lock works with the PCM, the security lockout actually causes the fuel injectors to be shut down, and this prevents starting. With a lot of security type problems, the vehicle will start for 2 seconds then shut off.
But the driving for 90 min and then an engine cut out points to a heat related fault.