New engine issues

EDIT Just saw the last line in your post, being the Thermoquad is removed already.
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That's a Thermoquad carb on that engine.
The strugling most likely comes from the secondaries opening up and things haven't been tuned properly when that happens.
the secondary airdoor has to be tuned so it opens gradually. If it's just flapping around or loose the engine will suddenly 'see' a big vacuum drop while no additional fuel-flow is initiated yet in the carb.

The slight miss should be taken care of first. Probably a lean mixture.
Someone needs a proper working (and willing) brain to tune a Thermoquad. This is why Holley's are so popular...
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The above still could apply if your current carb has a secondary 'air-valve'.