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Hmmmm.
Does this trans have any external controls??? Throttle cable/vacuum modulator??? Those could cause issues, but those are usually harsh shift issues.
If it's electronically controlled, I would suspect a sesnor on the new engine has issues.
Check the MAP, TPS, and MAF first off... basically any load calculating sensors..
Sounds like the comp isn't realizing it is as loaded down as it really is, and isn't making it shift as such.. That'd be my bet.
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