Holy crap Dalum, you have had it all happen to you. Do you have access to a 12v battery or a 12v power supply. I am with SwampRat something is fishy, I only started having issues when I had the car reprogrammed for the DRL function. Even then I didn't get a hyper flash issue. With the new ford adapters the amber will be dim at resting voltage, thats about it. You shouldn't really need the relays unless you are using the V3's as DRLs. When I did my first switchbacks (before the v3) I had the load resistors run across from the turn signal to the ground on the wiring harness (I still do with the relay setup). Not to the body and never had any issues. I am guessing you don't get hyper flash when you have a regular bulb in the socket? Could you tell me the actual current draw of the v3's with the builtin load resistors in place and are both units the same? There are also several different 3157 adapters (including the CK base) where the wiring is backwards to what ours should be and for obvious reasons can really mess with the car. I will be honest with you the relay is a PITA because of the external load resistors, if you are running DRL it's worth it. If there is no other way with your particular car I will be happy to help you set it up. But I would like to trouble shoot this a bit more before I would suggest you go that route. One last question was it happening on both units? Can you post pics of the adapters that Jake sent you? And your control boxes?
In the symptoms you have described above with the change from no hyper flash to hyper flash, the current draw sounds like it's dropping after the first few flashes. That to me would indicate that the V3s are disabling the internal load resistors for what ever reason. Again they should only do this while in DRL mode, Constant power to the amber part of the control unit. If you can bench test the units off the car, that would be a start. Give the turn signal input a constant 12V (without the adapter attached) You should get a reading, then after a second or so it should drop to about 1/2 of that. Then try pulsing the input and see if after a few pulses it changes. You could do this on the car, but with your history I would be cautious just in case you have a (or 2) defective control units. I would try to eliminate the control boxes first and then move onto the adapters.
I also have Forscan and I don't believe that the car throws a code when in hyper flash. It does throw a code when one of you headlights is out or in my case before the recent HID retrofit I was running some cheap HIDs. I had to run Canbus ballasts in order not to throw a code. I now run the Morimoto Canbus adapters to fool the car into thinking I have the halogen bulbs still in place.
I wish you were closer, I would be happy to give you a hand.