727 Issue With 2-3 Upshift

First hunch is your Bouchillon throttle-linkage is NOT following the factory-designed specs as to 'throw', ratio and distance from throttle-shaft center.
That's however more for stock-ish applications but you might look into it.

The throttle lever on the trans is the one from the Bouchillion kit as well as the carb adaptor, hooked up per their directions. 800cfm Edelbrock Thunder carb and adaptors.
I'm puzzled because there is no sweet spot in adjustment. The governor is being kept from working at wot.