Anyone here have any experience with the YZF-R bikes?

A buddy just gave his 2001 Yamaha R1 an engine swap. He mangled 2nd and 3rd gear in it at over 40,000 miles so instead of fixing the trans (which is something else... hahaha... you have to crack open the case) he just found another R1 motor.
Got it in and hooked everything up. The bike starts and runs, gets fuel, everything seems to be working... but the timing is off or something.
All 4 plugs are sparking, fuel seems to be fully delivered to the cylinders and everything seems to be as it should be. But they are saying it is running on 2 cylinders. I think it is running roughly but on all 4. It sounds like a harley when it is running but smooths out a bit at higher rpms.
I don't know much about the newer bikes... other than that they use a lot more computerized gadgets. As far as the motor, carb fed with a fuel delivery assist type of pump. in line 4 and not much different than any other in-line-four, liquid cooled motorcycle engine.

With the motor swap being done and everything obviously in the right place... where should we start and end with the trouble shooting and diagnosis of the poor running?

 

First place I'd start is to check all four cylinders for spark, eliminate the electrical system as a problem first. If it is only running on 2 cylinders, its probably there

 

Well we are getting spark on all cylinders. I am wondering if the intensity of the spark could be causing a problem. If a coil is going bad, etc. I mean... the whole bike had over 40,000 miles on it.
Also wondering if these carbs need balancing like our xj bikes or if that is done electronically.
So far it seems we have eliminated the problem being electrical.

 

Could still be coil packs. If you know anyone with a clamp on volt meter, find out if all 4 are getting the proper spark... 40K isn't THAT much, but 10 years is. The carbs probably need balancing like ours, the fuel management system iirc basically just keeps the float levels maintained for the amount of fuel being drawn.

How does the exhaust smell? Check and see if it smells gassy, you might not be getting a complete burn.

 

it does smell very rich.

 

I'd get those coils checked out then. Try doing a few low speed plug chops, preferably in the RPM range where it runs the worst. It sounds like 1 coil is gone and those plugs are probably getting rather wet.

Check the gapping while you're at it. They might need to be opened up a hundredth

 

I'll try the plug chops. The compression is good so it's not the cylinders. I wish it was an xj. Haha. It's too damn futuristic and technologically advanced.
I'm doing some online research on it.

 

My Ninja was only running on 2 cylinders when I first got it. Was getting spark on all 4,according to numbers on the wires they were all going to the right cylinders. After many hours of head scratching and checking things over I thought to follow the wires up to the coils. Sure enough someone had taken the wires out of the coils and put them back in the wrong spots. Had cylinders 1&2 going to one coil and 3&4 to the other. Should have been 1&4 and 2&3 together. Switched them around and she ran like a top.

 

I am totally going to check on that. I am going to laugh the rest of my arse off if that is the problem. Haha