If I do have them reversed how bad would the bike run?
Like a carbed bike! Hahaha!
Seriously, how long would it take you to swap the bike's harness feeds between the TFI counterparts, leaving the injector-proper connectors alone, for a test run? Maybe it'd be easier to swap only the connectors directly on the injectors? I'd think you'd think things were clearly the opposite of an improvement if you'd got the signals mixed up. One combination will noticeably differ from the other. Maybe not so much at idle, but certainly while running through the gears one combination will be clearly better than the other.
I just looked at a couple manuals at their site and they're quite clear that it doesn't matter which
order things are done in, but no mention of any special considerations. From what I can see of the photos of the unit, I'd think each pair of leads was a male/female for an injector. If that's the case and they're not cross-connected, it really shouldn't matter one iota which male/female pair went to which injector.
All it's doing is taking an injector signal and multiplying its duration by whatever factor is called-for at the time, then passing it along. If you cross-connected them, you'd have the injectors firing on the power strokes instead of the intake strokes. And the native fueling would pertain to the opposite cylinder. The cylinders don't have the same fuel curves as each other, so there would be some incorrectness in the base amount of fuel being delivered to each cylinder. That, coupled with the fuel being sprayed toward a closed intake valve would cause loss of atomization and possibly robbing of that present fuel by the other cylinder, since they share a common tract. It should
run, but not nearly so well as it could.
Seems their instructions would be a little more verbose about this.