That means you need to get your car tuned properly
The flashing CEL at about 15 second intervals means the ecu is trying to go into the "backup spark map." The reason I say "trying" is because your tuning/diagnostic connector has not been unplugged. After you're done tuning you unplug this to allow the ecu to engage the "backup spark" spark map which will be followed by a solid CEL when activated. Now, when the diagnostic connector is unplugged you cannot make real time changes or use ďautotune.Ē This is highlighted in your Hydra manual.
Most likely whatís happening is youíre misfiring now because of the more conservative ignition map. My guess is that your tuner ran the car so rich to prevent knock given the extremely advanced ignition curve that itís now misfiring which can be mistaken as knock by the ecu.
As for your idle itís not the ISC settings but inconsistent fueling across load sites. This takes time to dial in but if you watch your AFR closely when the idle oscillates you will see a change in AFR. Generally when the car goes leaner than 14.7 it will stumble so itís best to shoot for around 14:1 AFR. My guess is you have a lean spot in there which is causing the car to stumble. If youíve done this all correctly your idle should be no different than stock.