Check engine light when ECU Swap...???

Without the jumper, some good cycles, maybe 10 minutes. I'd personally start it up, let it idle on the stands, then shut it off.
Formerly cars; Honda's systems and manuals are all the same, and honestly quite dumped down on bikes compared to the crazy ass shit they're putting in cars now...well, that and I get bored and take my 600rr apart when I really shouldn't. I think my subconscious mind breaks things on purpose so I can fix it.

 

Another issue I've seen on the 600rr's with ECU swapping is if you have a CA bike it needs a CA ecu, if you have a non-CA bike, you need a non-CA ecu or it will throw codes just like you are describing...
2009 49 state bike is ecu PN: 38770-MFJ-A42 or 38770-MFJ-A43
2009 Calif bike is ecu PN: 38770-MFJ-L32

2008 49 state bike is ecu PN: 38770-MFJ-A02
2008 Calif bike is ecu PN: 38770-MFJ-L02

Also there are 2 small difference between the 08 & 09 main harnesses as well, shouldn't make any diffeence but...I can't say for sure. Which harness are you running?

 

Ok I got some help From NICO on the .net and he figured it out
knock sensor is wired differently...

A = Black connector
B = Light Grey connector

09:
Blue - B21
Blue/Yellow - B23
Yellow/Red - A9

08:
Blue - B21
Blue/Yellow - B5
Yellow/Red - A9

So wire it up the way it should be for an 08 ECU and you will be good to go!
Ok so now the big question?
How to I rewire the ecu?
How do I pull out the B23 cable and put it in B5?

 

Just pull the pin out from the back of the plug and pop it into the pin 5 slot. You might need to use a sewing needle or something to push down the tabs that hold it in. Found this on google; different plug, same concept.

 

Thanks Alot again Demented.....
I switched the pins and everything is 100%...!!!!
Thanks