You need to check the valves will turn easily, so drop the right mid panel off and see if you can rotate the pully wheel by hand.
The motor will offer some resistance, but it should be a smooth feeling from one endstop to the other. If it feels very hard or notchy you really shouldn't run the engine until you've had checked for carbon build up / correctly setup cables.
There are many many reasons for bad running, from the TPS to bad connections on the coils, jetting, powervalves, air filters, air leaks, and and and...
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MC21SP Plaything
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Triumph 9551 Daytona Big boys toy
FJ1100 Sporting relic
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