Checking head pipe temp (relational) tells you which cylinders are firing and how even they are among them. If unevenness is caused by carbs, the throttle position determines which jet is dominant for mixture control. This can also be a slide position issue related to carb balance.
Head pipe temps are another informational tool to help diagnose the proplem cause. If you had enough information, you'd know just what to fix, right?
Have you bench synced or vacuum balanced the carbs?
Have you accomplished the entire tune up procedure prior to carb meddling?
Have you looked at spark plug deposits to determine what's happening in the combustion chambers?
Cheers,