I will take a stab at this... I know Holley's new software not the old 950 ecm.
First, when you say it is going lean, at what time when you shift? My knee jerk reaction would be to say it would go rich when you let off the throttle and shift the gear. Unless it is going lean when you let off the clutch and push down on the throttle.
I would compare the lean spike to your throttle % and figure out the correlation.
If it is going lean when you let off the clutch and apply throttle I would try and fine and acceleration enrichment vs throttle % and try bumping it up in small increments.
Also when you let off the throttle there could be excess fuel so the ecm tries to pull to much when you are getting back on the throttle. See if there is a blanking value that would slow down the ecm's reaction to the rich condition.
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