60 seconds is adequate time to clear all OBDII info and DTC's that may be stored. I have seen cases where all the faults were cleared and when the battery was re-connected a fault still existed (because it still had a fault). It is very possible you still had a fault, wiring or loose pin and after some time of acclimating to weather conditions it cleared itself up before you re-connected the battery.

Probably not the best idea I have ever heard to disconnect the PCM with the battery still powered up, this can very easily lead to a voltage kick during hook up that will spike the PCM and render it junk.

Remember that clearing faults with the battery trick also clears all OBDII stored data including adaptive memory that stores things like fuel trim and IAC counter memory, it is common to have some drivability issues including idle surge, lack of performance, loss of fuel MPG and others while the system re-learns.

The best way to clear faults is with a proper scan tool that many parts stores will hook up and read/clear free of charge.

 

I can point you to dozens of people I know personally who clear their PCMs by unplugging it at the wiring harness. None of them have had any ill effects after nearly a decade and hundreds of resets. Can you show me just ONE person who spiked his PCM by doing this? If you can, I'll stop recommending it, but until then I say you're fine.

Just because the Mopar and Jet instructions say to disconnect the battery first when changing the PCM, doesn't mean it's a requirement. Don't ALL automotive procedures that deal with the engine compartment usually start with "disconnect the battery"? Most of the time, it's not nessicary, and unplugging the PCM is one of those instances. It's been proven to be safe for your PCM.

 

I used to disconnect the neg battery cable and turn the ignition key to start position and hold it there for 30 sec. This drains any copasiters(? spelling) holding voltage. Now I have a scanner that I picked up at Walmart. It was $98.00 and reads all OBDII systems as well as clears the codes. I have been very pleased with it's performance. Thats just my .02