Starting and running

I have a 2000 busa which i recently did a motor swap to a 2004. I changed everything besides the tb i kept the ones off of my 2000. When i try and start it is barely starts and when it does starts and sputters, Backfires and just runs like crap, also when you try to keep it running you can hear it popping to the air box and aslo out of the exhaust. Any held would really be appericated.

P.s. Does any one have a diagram on how the vacuum lines suppose to be hooked up??
You getting good strong spark on all plugs. I am probably saying all you have already tried. I'm just trying to run this list of things in my head. If you have good gas, sounds like it something one the sparkk side. Something giving you a dead miss.
That's all I have for right now. I'll do a little more thinking on it. Hopefully someone else will chime in and have something that's slipping our minds.
i had a power commander on the bike but i got messed up so i took it off and just ran the stock ecu with my other motor (2000) and it ran fine just not as responsive and i kept the same harness because everything matched up the same so i just kept it and i was going to use the 04 ecu but the fuel pump or what ever is in the tank and the 2000 is on the Tb so had to use the 2000 ECU so pump would come on....

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