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The IDI neither needs nor uses any input from the PCM to start and run, so I believe your no-start condition is caused by a bad contact in the engine harness - check those connectors inside the engine on the driver-side of the firewall, maybe you knocked something loose accidentally?
The other problem is caused by the PCM entering "limp-home" mode, essentially if you throw the switch on and lock the converter whenever the PCM commands it to be open this will be interpreted as an electrical failure and the PCM will switch to failure-management aka "limp-home" mode and you will only have 2nd and 4th unlocked. It's a hit or miss deal, some trucks don't do this but many do, so I guess that makes your situation sorta part of the norm. To avoid this when you want to manually control the lockup you need to have the PCM connection severed from the lockup solenoid harness and you need to feed the PCM a "dummy" signal. Stay tuned for a wiring diagram for this...
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