If I was to replace the FI ECU does it need to be reflashed to operate on my bike? No, it needs to be registered to KIPASS using KDS or the bike will not start - mimicking the problem you already have.
As you're not getting any fault codes when you seemed to get the ignition to turn on, I know of no other way of checking for a faulty FI ECU, short of sending it off to a specialist.
I don't like to throw money/parts at a problem but in this case I would make an exception (given that the ebay item above is less than $100) in the absence of rodent damage, which to my mind, is highly probable given what you discovered behind the battery. I would remove the tank and some plastic to have a thorough look everywhere on the bike.