Most Windows installs nowadays come with FTDI drivers already pre-loaded. In that case it's as simple as running the software and plugging the device in. Be sure to watch the tutorial video for guidance.
This would be the correct file for you currently. You unfortunately have not gotten Honda's update to the newer software and won't have additional advanced features until you do. There's also a CVT controller update, which is why you can't run the newer software version by just flashing it in.
It's not the tune on the unit that it's reverting to, like Tuning Slot 1 for instance.
If you setup the map switching feature in the tune that you uploaded, you can switch on the fly between those options. That defaults to map 1 if you don't have the unit connected...
You disabled ECT2 to use it for flex. It's no longer used in factory capacity.
If ECT 1 was affected that's likely due to your wiring issue, which you solved. Not sure what more needs focused on there.